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PDB ID Mentions in PubMed Central Article count: 21

Citations in PubMed

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PDB ID Mentions in PubMed Central

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Ligation site in proteins recognized in silico.

(2006) Bioinformation 1

PubMed: 17597871 | PubMedCentral: PMC1891674 | DOI: null

Methodology Data Complexes selected for analysis presented in this paper are: cAMP-dependent protein kinase (PDB ID: 1CDK), cyclin-dependent protein kinase 2 (PDB ID: 1E1V), proto-oncogene tyrosine-pr... tein kinase ABL (PDB ID: 1IEP), S-lectin (PDB ID: 1SLT).

Publication Year: 2006


Protein functional surfaces: global shape matching and local spatial alignments of ligand binding sites.

(2008) BMC Struct Biol 8

PubMed: 18954462 | PubMedCentral: PMC2626596 | DOI: 10.1186/1472-6807-8-45

d]pyrimidine-type (PDB: 1m52 , 1opk ) and 2-phenylaminopyrimidine-type (PDB: 1iep , 1fpu , 1opj ).

Publication Year: 2008


The structure of the leukemia drug imatinib bound to human quinone reductase 2 (NQO2).

(2009) BMC Struct Biol 9

PubMed: 19236722 | PubMedCentral: PMC2655291 | DOI: 10.1186/1472-6807-9-7

A) The structure of imatinib bound to the kinase domain of Abl (PDB ID 1IEP ) [ 6 ].

Publication Year: 2009


Exploiting the promiscuity of imatinib.

(2009) J Biol 8

PubMed: 19435483 | PubMedCentral: PMC2689438 | DOI: 10.1186/jbiol134

Figure 1 Atomic interactions of imatinib with (a) NQO2 (Protein Data Bank (PDB) code 1FW3 ) and (b) ABL kinase domain (PDB 1IEP ).

The structure of imatinib (from PDB 1IEP ) is shown in the middle, with carbon (green), nitrogen (blue) and oxygen (red) atoms displayed.

Publication Year: 2009


Hierarchical modeling of activation mechanisms in the ABL and EGFR kinase domains: thermodynamic and mechanistic catalysts of kinase activation by cancer mutations.

(2009) PLoS Comput Biol 5

PubMed: 19714203 | PubMedCentral: PMC2722018 | DOI: 10.1371/journal.pcbi.1000487

MD Simulations MD simulations of the ABL kinase domain were independently launched for ABL-WT, ABL-T315I and ABL-L387M from the inactive form (pdb entry 1IEP), Src-like structure (pdb entry 2G1T) and ... ctive state (pdb entry 1M52).

Materials and Methods Structure Preparation In simulations of the ABL and EGFR kinase domains, we used the following crystal structures from the Protein Data Bank (PDB): pdb entry 1IEP (inactive ABL structure), pdb entry 2G1T (Src-like inactive ABL structure), pdb entry 1M52 (active ABL structure), pdb entry 1XKK (Src/Cdk-like inactive EGFR structure), pdb entry 2GS7 (Src/Cdk-like inactive EGFR structure) and pdb entry 2J6M (active EGFR structure).

The crystal structures of ABL represent the following conformational forms: the Imatinib-bound, inactive structure (pdb entry 1IEP) (A), the Src-like inactive structure (pdb entry 2G1T) (B), and the active structure (pdb entry 1M52) (C).

TMD simulations were carried out for ABL-WT, ABL-T315I and ABL-L387M to model conformational transitions from the Imatinib-bound, inactive state of ABL (pdb entry 1IEP) to the target active ABL conformation (pdb entry 1M52 for ABL-WT and ABL-L387M; pdb entry 2Z60 for ABL-T315I).

Publication Year: 2009


Masitinib (AB1010), a potent and selective tyrosine kinase inhibitor targeting KIT.

(2009) PLoS One 4

PubMed: 19789626 | PubMedCentral: PMC2746281 | DOI: 10.1371/journal.pone.0007258

Molecular modelling X-ray coordinates of the STI571/ABL (1IEP.

Publication Year: 2009


Sequence and structure signatures of cancer mutation hotspots in protein kinases.

(2009) PLoS One 4

PubMed: 19834613 | PubMedCentral: PMC2759519 | DOI: 10.1371/journal.pone.0007485

The kinase catalytic domain was subdivided into 12 subdomains (SD) using the ABL kinase crystal structure (pdb entry 1IEP) as the reference for defining the residue ranges as follows : SD I:242ȁ... ;261(P-loop region); SD2 :262–278; SD3:279–291(αC-helix); SD4:292–309; SD5:310–335 (hinge region); SD6A:336–356; SD6B357–374 (catalytic loop); SD7:375–393 (activation loop) ; SD8:394–416 (P+l loop); SD9:417–438; SD10:439–461; SD11:462–480; SD12:481–498.

Publication Year: 2009


Interplay between kinase domain autophosphorylation and F-actin binding domain in regulating imatinib sensitivity and nuclear import of BCR-ABL.

(2011) PLoS One 6

PubMed: 21347248 | PubMedCentral: PMC3037956 | DOI: 10.1371/journal.pone.0017020

A : Position of tyrosines 232, 253, and 257 as seen in a crystal structure of the ABL kinase domain bound to imatinib ( [31] , PDB code 1IEP).

Publication Year: 2011


Crystal structures of ABL-related gene (ABL2) in complex with imatinib, tozasertib (VX-680), and a type I inhibitor of the triazole carbothioamide class.

(2011) J Med Chem 54

PubMed: 21417343 | PubMedCentral: PMC3075623 | DOI: 10.1021/jm101506n

The structure of the active site of ABL1 with imatinib bound (blue) (PDB code 1IEP )( 22 ) is shown superimposed on ABL2:imatinib (orange), showing that the inhibitor molecules bind in the same confor... ation in both structures.

The molecule of imatinib bound to the active site is in the same conformation as reported for the imatinib:ABL1 complex (PDB code 1IEP ) (Figure 2 A), and the structures were superimposed with an rmsd of 0.61 Å over 258 Cα atoms.

Publication Year: 2011


Predicting inactive conformations of protein kinases using active structures: conformational selection of type-II inhibitors.

(2011) PLoS One 6

PubMed: 21818358 | PubMedCentral: PMC3144914 | DOI: 10.1371/journal.pone.0022644

Kinases PDB codes Numbers of occupied water molecules ABL1 1FPU 46 1IEP 49 1OPJ 50 2HIW 41 2HYY 43 2HZ0 33 2HZN 45 KIT 1T46 43 LCK 2PL0 45 MK14 1W82 44 1W83 35 1WBN 45 1WBS 44 1WBT 42 1WBV 39 2BAJ 44 ... redictions of kinase DFG-out models For each protein kinase listed in Table 1 , we employed the ALRM approach illustrated in Fig. 2A to generate 200 lowest-energy models using its corresponding DFG-in structure, and then classified them into DFG-in or DFG-out models according to the method described in Materials and Methods .

>GIN(2HZ0), KIN(2HZN), PRC(1FPU), STI(1IEP, 1OPJ, 2HYY) BRAF1 2FB8(A,B) BAX(1UWH, 1UWJ) EPHA3 2QOQ(A) IFC(3DZQ) KIT 1PKG(A,B) STI(1T46) LCK 3LCK(A) 1N8(2OG8), 242(2OFV), 9NH(3B2W), STI(2PL0) MK14 1M7Q(A) 1PP(2BAJ), AQZ(2BAK), B96(1KV2), BMU(1KV1), L09(1WBN), L10(1W82), L11(1W83), LI2(1WBS), LI3(1WBV), WBT(1WBT) SRC 1Y57(A) STI(2OIQ) Results and Discussion Outward movements of N-lobes in DFG-out structures We searched the Protein Dada Bank (PDB) at the beginning of this study and found seven kinases with both the DFG-in and DFG-out structures, as listed in Table 1 .

Publication Year: 2011


Computational modeling of allosteric communication reveals organizing principles of mutation-induced signaling in ABL and EGFR kinases.

(2011) PLoS Comput Biol 7

PubMed: 21998569 | PubMedCentral: PMC3188506 | DOI: 10.1371/journal.pcbi.1002179

In MD simulations of the ABL and EGFR kinase domains, we used the following crystal structures : PDB ID 1IEP (inactive ABL structure) [70] , PDB ID 1M52 (active ABL structure) [71] , [72] , PDB ID 2G1... (Src-like inactive ABL structure) [109] , PDB ID 2Z60 (the active form of the ABL-T315I mutant) [75] , PDB ID 1XKK (Src/Cdk-like inactive EGFR structure) [77] , PDB ID 2GS7 (Src/Cdk-like inactive EGFR structure) [109] , and PDB ID 2J6M (active EGFR structure) [78] , and PDB ID 2JIT (EGFR-T790M mutant) [79] .

Structural mapping of residues involved in long-range communication in different functional states of the ABL catalytic domain: ( A ) the inactive ABL-WT structure (PDB ID 1IEP); ( B ) the active ABL-WT structure (PDB ID 1M52); ( C ) the active form of the ABL-T315I mutant (PDB ID 2Z60).

Allosteric Signatures of Mutation-Induced ABL Activation In this section, we analyzed collective motions and long-range communications in the ABL kinases using the results of our recently reported simulations of the ABL catalytic domain and multidomain complexes [155] in the following functional states: inactive ABL state (PDB ID 1IEP) [70] , the active ABL state (PDB ID 1M52) [71] , [72] ; the active form of the ABL-T315I mutant (PDB ID 2Z60) [75] ; the inactive autoinhibited form of ABL-SH2-SH3 complex (PDB ID 2FO0) and the active form of the ABL complex (PDB ID 1OPL) [108] .

Publication Year: 2011


The energy landscape analysis of cancer mutations in protein kinases.

(2011) PLoS One 6

PubMed: 21998754 | PubMedCentral: PMC3188581 | DOI: 10.1371/journal.pone.0026071

The analysis was performed using inhibitor-bound crystal structures of ABL in the inactive form (PDB ID 1IEP) [ 90 ] and active form (PDB ID 1M52) [ 91] , [92 ] .

The analysis was performed on the unbound form of the crystal structures of ABL in the inactive form (PDB ID 1IEP) [ 90 ] and active form (PDB ID 1M52) [ 91] , [92 ] .

Structural mapping of local frustration on the ABL kinase catalytic core is shown for the inactive ABL-WT structure (PDB ID 1IEP) [ 90 ] and active ABL-WT structure (PDB ID 1M52) [ 91] , [92 ] .

We observed that highly oncogenic mutations may indeed cause an increase in the local frustration of mutated residues in the inactive autoinhibitory state of ABL (PDB ID 1IEP) [ 90 ] and EGFR (PDB ID 1XKK) [ 117 ] ( Figures 3 , 4 ).

Structural mapping of local frustration on the ABL kinase catalytic core is shown for the inactive ABL-WT structure (PDB ID 1IEP) [ 90 ] .

The residue ranges of the kinase subdomains (SD) were determined based on the ABL kinase crystal structure (PDB ID 1IEP) [90] as the reference and in accordance to our previous study [123] : SDI:242-261(P-loop region); SD2:262-278; SD3:279-291(αC-helix); SD4:292-309; SD5:310-335 (hinge region); SD6A:336-356; SD6B357-374 (catalytic loop); SD7:375-393 (activation loop); SD8:394-416 (P+l loop); SD9:417-438; SD10:439-461; SD11:462-480; SD12:481-498.

The set of inactive kinase conformations included ABL (PDB 1IEP), KIT (PDB ID 1T45), MET (PDB ID 2G15) and BRAF (PDB ID 1UWH).

Publication Year: 2011


Structural and spectroscopic analysis of the kinase inhibitor bosutinib and an isomer of bosutinib binding to the Abl tyrosine kinase domain.

(2012) PLoS One 7

PubMed: 22493660 | PubMedCentral: PMC3320885 | DOI: 10.1371/journal.pone.0029828

E) The conformation of the P-loop in our structure (shown in yellow, the two disordered residues are indicated as a dashed yellow line), compared to that observed in the imatinib cocrystal structure (... db code 1IEP, shown in gray), and a substrate complex of Abl (pdb code 2G1T, shown in brown).

Publication Year: 2012


Nilotinib based pharmacophore models for BCRABL.

(2012) Bioinformation 8

PubMed: 23055606 | PubMedCentral: PMC3449370 | DOI: 10.6026/97320630008658

Methodology C-ABL KINASE DOMAIN IN COMPLEX WITH STI-571 was downloaded (1IEP) from PDB database [ 18 ].

Citation: Sabitha, Bioinformation 8(14): 658-663 (2012) References 1 CR Bartram Nature 1983 306 277 6580527 2 J Groffen Cell 1984 36 93 6319012 3 TG Lugo Science 1990 247 1079 2408149 4 C Gambacorti-Passerini Blood 2003 102 1933 12930735 5 E Weisberg Nat Rev Cancer 2007 7 345 17457302 6 T Hughes Blood 2006 108 28 16522812 7 N Moitessier Br J Pharmacol 2008 26 S7 18037925 8 DB Kitchen J Nat Rev Drug Discov 2004 3 935 15520816 9 RT Kroemer Curr Protein Pept Sci 2007 8 312 17696866 10 BO Villoutreix Curr Protein Pept Sci 2007 8 381 17696871 11 CN Cavasotto Curr Top Med Chem 2007 7 1006 17508934 12 C McInnes Curr Opin Drug Discov Devel 2006 9 339 16729730 13 CN Cavasotto RA Abagyan J Mol Biol 2004 337 209 15001363 14 DM Lorber Protein Sci 2002 11 1393 12021438 15 Chang Yeong-Sheng Journal of Chinese Chemical Society 2010 57 916 16 Wolber Gerhard Drug Discovery Today 2008 13 23 18190860 17 http://www.scfbio-iitd.res.in/ 18 http://www.rcsb.org/pdb/explore/explore.do?structureI d=1IEP 19 W Brooks J Chem INF Model 2008 48 639 18266348 20 http://pubchem.ncbi.nlm.nih.gov/ 21 RA Friesner J Med Chem 2004 47 1739 15027865 22 TA Halgren J Med Chem 2004 47 1750 15027866 23 R Wang J Comput Aided Mol Des 2002 16 11 12197663 24 J Huuskonen SAR QSAR Environ Res 2008 19 191 18484495 25 EM Duffy WL Jorgensen J Am Chem Soc 2000 122 2878 Figure 1 C-ABL KINASE DOMAIN (1IEP) structure predicted by X-ray crystallography , Hydrogen bonds are added, protonation states of residues are corrected and energy minimized by Schrodinger Protein preparation wizard.

Publication Year: 2012


Modelling dynamics in protein crystal structures by ensemble refinement.

(2012) Elife 1

PubMed: 23251785 | PubMedCentral: PMC3524795 | DOI: 10.7554/eLife.00311

( A ) Imatinib binding site in chain A of the 1IEP dataset showing distribution of the six protein–ligand hydrogen bonds in chain A and chain B (red and blue respectively).

Comparison of atomic fluctuations for NCS related protein copies for dataset 1IEP.

The PDB accession numbers are as follows: 1KZK ( Reiling et al., 2002 ), 3K0M ( Fraser et al., 2009 ), 3K0N ( Fraser et al., 2009 ), 2PC0 ( Heaslet et al., 2007 ), 1UOY ( Olsen et al., 2004 ), 3CA7 ( Klein et al., 2008 ), 2R8Q ( Wang et al., 2007 ), 3QL0 ( Bhabha et al., 2011 ), 1X6P ( Dunlop et al., 2005 ), 1F2F ( Kimber et al., 2000 ), 3QL3 ( Bhabha et al., 2011 ), 1YTT ( Burling et al., 1996 ), 3GWH ( Rodríguez et al., 2009 ), 1BV1 ( Gajhede et al., 1996 ), 1IEP ( Nagar et al., 2002 ), 2XFA ( Singh et al., 2011 ), 3ODU ( Wu et al., 2010 ), 1M52 ( Nagar et al., 2002 ), 3CM8 ( He et al., 2008 ) and 3RZE ( Shimamura et al., 2011 ) DOI: http://dx.doi.org/10.7554/eLife.00311.003 PDB ID Resolution (Å) Ensemble refinement phenix.refine Ensemble—phenix.refine τ x (ps) No.

Rms ( m F obs − DF model )exp[ iφ model ] difference densities obtained from ensemble refinement and re-refinement in phenix.refine DOI: http://dx.doi.org/10.7554/eLife.00311.006 PDB ID Resolution (Å) σ mFo−DFc (e/Å 3 ) Ensemble phenix.refine 1KZK 1.1 0.138 0.161 3K0M 1.3 0.016 0.018 3K0N 1.4 0.007 0.008 2PCO 1.4 0.099 0.099 1UOY 1.5 0.115 0.162 3CA7 1.5 0.132 0.148 2R8Q 1.5 0.104 0.118 3QL0 1.6 0.124 0.138 1X6P 1.6 0.098 0.105 1F2F 1.7 0.104 0.126 3QL3 1.8 0.131 0.139 1YTT 1.8 0.170 0.215 3GWH 2.0 0.125 0.138 1BV1 2.0 0.109 0.119 1IEP 2.1 0.084 0.091 2XFA 2.1 0.069 0.074 3ODU 2.5 0.105 0.113 1M52 2.6 0.088 0.093 3CM8 2.9 0.036 0.036 3RZE 3.1 0.070 0.070 10.7554/eLife.00311.007 Table 3.

Additional files Major datasets The following datasets were generated Burnley BT , Afonine PV , Adams PD , Gros P , 2012 , Data from: Modelling dynamics in protein crystal structures by ensemble refinement , http://dx.doi.org/10.5061/dryad.5n01h , Available at Dryad Digital Repository The following previously published datasets were used: Reiling KK , Endres NF , Dauber DS , Craik CS , Stroud RM , 2002 , JE-2147-HIV Protease Complex , 1KZK ; Publically available at the RCSB Protein Data Bank ( http://www.rcsb.org/pdb/ ) Fraser JS , Clarkson MW , Degnan SC , Erion R , Kern D , Alber T , 2009 , Cryogenic structure of CypA , 3K0M ; Publically available at the RCSB Protein Data Bank ( http://www.rcsb.org/pdb/ ) Fraser JS , Clarkson MW , Degnan SC , Erion R , Kern D , Alber T , 2009 , Room temperature structure of CypA , 3K0N ; Publically available at the RCSB Protein Data Bank ( http://www.rcsb.org/pdb/ ) Heaslet H , Rosenfeld R , Giffin M , Lin YC , Tam K , Torbett BE , Elder JH , McRee DE , Stout CD , 2007 , Apo Wild-type HIV Protease in the open conformation , 2PC0 ; Publically available at the RCSB Protein Data Bank ( http://www.rcsb.org/pdb/ ) Olsen JG , Flensburg C , Olsen O , Bricogne G , Henriksen A , 2004 , The Bubble Protein from Penicillium brevicompactum Dierckx Exudate , 1UOY ; Publically available at the RCSB Protein Data Bank ( http://www.rcsb.org/pdb/ ) Klein DE , Stayrook SE , Shi F , Narayan K , Lemmon MA , 2008 , High Resolution Crystal Structure of the EGF domain of spitz , 3CA7 ; Publically available at the RCSB Protein Data Bank ( http://www.rcsb.org/pdb/ ) Wang H , Yan Z , Geng J , Kunz S , Seebeck T , Ke H , 2007 , Structure of LmjPDEB1 in complex with IBMX , 2R8Q ; Publically available at the RCSB Protein Data Bank ( http://www.rcsb.org/pdb/ ) Bhabha G , Lee J , Ekiert DC , Gam J , Wilson IA , Dyson HJ , Benkovic SJ , Wright PE , 2011 , Crystal structure of N23PP/S148A mutant of E. coli dihydrofolate reductase , 3QL0 ; Publically available at the RCSB Protein Data Bank ( http://www.rcsb.org/pdb/ ) Dunlop KV , Irvin RT , Hazes B , 2005 , Structure 4; room temperature crystal structure of truncated pak pilin from Pseudomonas aeruginosa at 1.63A resolution , 1X6P ; Publically available at the RCSB Protein Data Bank ( http://www.rcsb.org/pdb/ ) Kimber MS , Nachman J , Cunningham AM , Gish GD , Pawson T , Pai EF , 2000 , SRC SH2 ThrEF1Trp Mutant , 1F2F ; Publically available at the RCSB Protein Data Bank ( http://www.rcsb.org/pdb/ ) Bhabha G , Lee J , Ekiert DC , Gam J , Wilson IA , Dyson HJ , Benkovic SJ , Wright PE , 2011 , Re-refined coordinates for PDB entry 1RX2 , 3QL3 ; Publically available at the RCSB Protein Data Bank ( http://www.rcsb.org/pdb/ ) Burling FT , Weis WI , Flaherty KM , Brunger AT , 1996 , Yb substituted subtilisin fragment of mannose binding protein A (Sub-MBP-A), MAD structure at 110K , 1YTT ; Publically available at the RCSB Protein Data Bank ( http://www.rcsb.org/pdb/ ) Rodriguez DD , Grosse C , Himmel S , Gonzalez C , de Ilarduya IM , Becker S , Sheldrick GM , Uson I , 2009 , Crystallographic Ab Initio protein solution far below atomic resolution , 3GWH ; Publically available at the RCSB Protein Data Bank ( http://www.rcsb.org/pdb/ ) Gajhede M , Osmark P , Poulsen FM , Ipsen H , Larsen JN , Joost van Neerven RJ , Schou C , Lowenstein H , Spangfort MD , 1996 , Birch pollen allergen Bet V 1 , 1BV1 ; Publically available at the RCSB Protein Data Bank ( http://www.rcsb.org/pdb/ ) Nagar B , Bornmann W , Pellicena P , Schindler T , Veach DR , Miller WT , Clarkson B , Kuriyan J , 2002 , Crystal structure of the C-Abl Kinase domain in complex with STI-571 , 1IEP ; Publically available at the RCSB Protein Data Bank ( http://www.rcsb.org/pdb/ ) Singh BK , Sattler JM , Chatterjee M , Huttu J , Schuler H , Kursula I , 2011 , Crystal structure of Plasmodium berghei actin depolymerization Factor 2 , 2XFA ; Publically available at the RCSB Protein Data Bank ( http://www.rcsb.org/pdb/ ) Wu B , Chien EY , Mol CD , Fenalti G , Liu W , Katritch V , Abagyan R , Brooun A , Wells P , Bi FC , Hamel DJ , Kuhn P , Handel TM , Cherezov V , Stevens RC , 2010 , The 2.5 A structure of the CXCR4 chemokine receptor in complex with small molecule antagonist IT1t , 3ODU ; Publically available at the RCSB Protein Data Bank ( http://www.rcsb.org/pdb/ ) Nagar B , Bornmann W , Pellicena P , Schindler T , Veach DR , Miller WT , Clarkson B , Kuriyan J , 2002 , Crystal Structure of the c-Abl Kinase domain in complex with PD173955 , 1M52 ; Publically available at the RCSB Protein Data Bank ( http://www.rcsb.org/pdb/ ) He X , Zhou J , Bartlam M , Zhang R , Ma J , Lou Z , Li X , Li J , Joachimiak A , Zeng Z , Ge R , Rao Z , Liu Y , 2008 , A RNA polymerase subunit structure from virus , 3CM8 ; Publically available at the RCSB Protein Data Bank ( http://www.rcsb.org/pdb/ ) Shimamura T , Shiroishi M , Weyand S , Tsujimoto H , Winter G , Katritch V , Abagyan R , Cherezov V , Liu W , Han GW , Kobayashi T , Stevens RC , Iwata S , 2011 , Structure of the human histamine H1 receptor in complex with doxepin , 3RZE ; Publically available at the RCSB Protein Data Bank ( http://www.rcsb.org/pdb/ ) References Adams PD Afonine PV Bunkóczi G Chen VB Davis IW Echols N 2010 PHENIX: a comprehensive Python-based system for macromolecular structure solution .

Publication Year: 2012


CREDO: a structural interactomics database for drug discovery.

(2013) Database (Oxford) 2013

PubMed: 23868908 | PubMedCentral: PMC3715132 | DOI: 10.1093/database/bat049

pmatch=*/STI* for example shows a list of all Imatinib ligands currently in CREDO, whereas/ligands/1IEP/1/B/STI`202 will return the overview page for the corresponding ligand from PDB entry 1IEP.

Publication Year: 2013


Ponatinib is a pan-BCR-ABL kinase inhibitor: MD simulations and SIE study.

(2013) PLoS One 8

PubMed: 24236021 | PubMedCentral: PMC3827254 | DOI: 10.1371/journal.pone.0078556

Figure S2 The alignment of the C-alpha helix from imatinib bound BCR-ABL PDB_ID:1IEP (magenta) and Ponatinib bound BCR_ABL PDB_ID:3OXZ (Cyan) (A).

g005 Figure 5 Structure alignment of imatinib bound BCR-ABL kinase (PDB_ID: 1IEP) (green) and ponatinib bound BCR-ABL kinase (PDB_ID: 3OXZ) (blue).

Publication Year: 2013


LIBSA--a method for the determination of ligand-binding preference to allosteric sites on receptor ensembles.

(2014) J Chem Inf Model 54

PubMed: 24437606 | PubMedCentral: PMC3985772 | DOI: 10.1021/ci400474u

1IEP 1.9e5 225 (0.25) 7 1.05 Gleevec p38 MAPK 3GP0 2.1e5 225 (0.25) 7 1.05 a Because the available Ras ligands are reportedly nonspecific for the highly homologous Ras isoforms, 27 , 2... for a stringent test of LIBSA we docked ligands solved with the K-Ras isoform on two PDB and an MD apo structure of H-Ras.

Publication Year: 2014


Exploration of type II binding mode: A privileged approach for kinase inhibitor focused drug discovery?

(2014) ACS Chem Biol 9

PubMed: 24730530 | PubMedCentral: PMC4068218 | DOI: 10.1021/cb500129t

(C) Imatinib complexes with Abl (PDB ID: 1IEP) in type II binding.

(D) Demonstration of DFG-out A-loop-L (direct to Hinge) conformation (PDB ID: 1IEP).

Publication Year: 2014


Computational methods for analysis and inference of kinase/inhibitor relationships.

(2014) Front Genet 5

PubMed: 25071826 | PubMedCentral: PMC4075008 | DOI: 10.3389/fgene.2014.00196

Only the ribbon representation of the human ABL kinase domain from 1IEP (chain A) is shown.

The human ABL kinase co-crystallized with imatinib (PDB code 1IEP) was used as reference for the structural superposition of the human ABL co-crystallized with dasatinib (PDB code 2GQG) and of the mouse ABL in complex with the allosteric inhibitor GNF-2 (PDB code 3K5V).

Publication Year: 2014


PubMed ID is not available.

Published in 2014

PubMedCentral: PMC4383952

Captured image from the superimposition viewer, which shows the superimposition of an STI-binding pocket of 1IEP to a putative pocket of 2GK9.

We present an example here: similarity between the imatinib (HET: STI)-binding pocket of the tyrosine protein kinase ABL (PDB ID: 1IEP) ( 23 ) and a putative pocket of phosphatidylinositol-4-phosphate 5 (P4P5)-kinase (PDB ID: 2GK9).

Publication Year: 2014