Primary Citation PubMed: 10988075
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Structural biology contributions to the discovery of drugs to treat chronic myelogenous leukaemia.
(2007) Acta Crystallogr D Biol Crystallogr 63
PubMed: 17164530 | PubMedCentral: PMC2483489 | DOI: 10.1107/S0907444906047287
Structure determination and refinement Structures were determined using MOLREP from the CCP 4 program interface CCP 4 i (Vagin & Teplyakov, 1997 ▶ ; Collaborative Computation... l Project, Number 4, 1994 ▶ ), initially using the protein coordinates of PDB entry 1fpu (Schindler et al. , 2000 ▶ ) and then using the most similar structures obtained in our laboratory.
Publication Year: 2007
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
Structure-based drug design and AutoDock study of potential protein tyrosine kinase inhibitors.
(2011) Bioinformation 5
PubMed: 21383902 | PubMedCentral: PMC3044423 | DOI: null
Thus herein compound VIIIb, N3- phenyl-8-chloro-N10-(3, 4-xylyl)-5-deazaflavin, was tested for docking into Abelson tyrosine kinase (ABL, pdb code: 1fpu) to find potential inhibitor candidate.
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
>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) M... 14 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 .
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 Predictions 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 .
Kinases PDB codes of DFG-out structures Structural resolution (Å) Numbers and percentages of DFG-out models Populations of DFG-out clusters ≥5 Global TM-score DFG motif RMSD (Å) Average Maximum Average Minimum ABL1 1FPU 2.40 104 (52%) 52, 20, 10, 6 0.86 0.89 4.48 1.64 BRAF1 1UWH 2.95 67 (34%) 41, 13, 5, 5 0.87 0.88 4.45 1.45 EPHA3 3DZQ 1.75 101 (51%) 68, 17, 7 0.90 0.91 5.71 1.51 KIT 1T46 1.60 67 (34%) 39, 12, 6, 5 0.88 0.90 5.39 2.03 LCK 2PL0 2.80 102 (51%) 56, 21, 7, 6 0.89 0.92 4.59 1.98 MK14 1WBT 2.00 61 (31%) 41, 9 0.95 0.97 5.02 2.03 SRC 2OIQ 2.07 109 (55%) 56, 23, 11, 7 0.96 0.97 2.75 0.60 It is well known that the activation-loops of PKs are flexible segments.
Also, flexibility means that the activation-loops may explore multiple conformations in a dynamic way and possess certain conformational diversity, for example, the activation-loop of ABL1 in the DFG-out conformation has been observed to adopt two very different conformations (see details in PDB codes: 1FPU and 2HZ0).
An aggregate analysis of many predicted structures to reduce errors in protein structure comparison caused by conformational flexibility.
(2013) BMC Struct Biol 13 Suppl 1
PubMed: 24564934 | PubMedCentral: PMC3952246 | DOI: 10.1186/1472-6807-13-S1-S10
Enolase Superfamily (homogeneous): Enolases: 1e9i , 1iyx , 1pdy , 2pa6 , 2xsx , 2xsx Enolase Superfamily (homogeneous, redundant): Enolases: 1ebh , 1els , 1nel , 2al2 , 3enl , 7enl , 1te6 , 1ebg , 1on... Tyrosine Kinases (homogeneous): Small Gatekeeper residue: 1qcf , 1fgi , 1fpu , 1fvr , 1gjo , 1irk , 1k2p , 1m14 , 1m7n , 1qpc , 1r0p , 1t45 , 1u4d , 1yvj , 1ywn , 2src Tyrosine Kinases (homogeneous, redundant): Small Gatekeeper residue: 2hz4 , 2e2b , 2hyy , 2hz0 , 2hzn , 2hzi , 2xyn , 2hmi , 3kf4 , 3kfa , 3ms9 , 3mss Enolase Superfamily (heterogeneous): Enolases: 1e9i , 1ebh , 1iyx , 1pdy , 1te6 , 2pa6 , 2xsx , 3otr , Mandelate Racemase: 2ox4 , Muconate Lactonizing Enzyme: 2pgw , 2zad Tyrosine Kinases (heterogeneous): Small Gatekeeper residue: 2hz4 Large Gatekeeper residue: 1fvr , 1luf , 1rjb , 1sm2 , 1snu , 1snx Bolded structures were selected as templates.
Publication Year: 2013
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