Citations in PubMed

Primary Citation PubMed: 15181000 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 11

Citations in PubMed

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PDB ID Mentions in PubMed Central

Data mentions are occurrences of PDB IDs in the full text articles from the PubMedCentral Open Access Subset of currently about 1 million articles. For each article, the sentences containing the PDB ID are listed. Article titles can be filtered by keywords and sorted by year.

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The role of hydrophobic interactions in positioning of peripheral proteins in membranes.

(2007) BMC Struct Biol 7

PubMed: 17603894 | PubMedCentral: PMC1934363 | DOI: 10.1186/1472-6807-7-44

Protein Category Conformation 1 a Conformation 2 a PDB id Δ G calc D τ PDB id Δ G calc D τ Signal peptidase A.1 1kn9 -4.5 4.5 83 1t7d -5.9 3.7 66 Cytochrome P450 2b4 A.... 1po5 -6.9 9.7 39 2bdm -18.2 10.5 45 Cytochrome P450 2c5 A.1 1nr6 -11.6 12.5 54 1dt6 -8.4 7.5 17 Cytochrome P450 2c9 A.1 1og5 -13.6 7.5 74 1r9o -10.7 7.5 57 Cytochrome P450 3a4 A.1 1tqn -20.7 10.2 61 1w0f -15.2 6.2 68 Bile-salt activated lipase C.1 1aql -9.7 6.0 80 1akn -6.6 5.7 67 Triacylglycerol lipase C.1 1tib -3.3 1.9 42 1dt5 -4.8 2.9 84 Lipase/colipase complex C.1 1lpa -22.1 8.7 89 1lpb -26.2 10.3 87 Ganglioside GM2 activator C.2 1tjj -9.3 4.6 55 1pub -7.8 5.2 44 Phosducin/βγ complex C.3 1a0r -3.7 2.7 45 2trc -2.9 4.4 64 Tubby protein C.4 1c8z -4.2 6.2 87 1i7e -3.6 2.6 78 a All structures were solved by X-ray crystallography.

Publication Year: 2007


Automated docking screens: a feasibility study.

(2009) J Med Chem 52

PubMed: 19719084 | PubMedCentral: PMC2745826 | DOI: 10.1021/jm9006966

There were three nuclear receptors ( 1M2Z , 1N46 , 1SQN ), six kinases ( 1KE5 , 1OPK , 1YWR , 1V4S , 1PMN , 1T46 ), and seven other enzymes ( 1HWI , 1OF6 , 1LPZ , 1Q4G , 1JLA , 1R9O , 1VCJ ).

Publication Year: 2009


SuperCYP: a comprehensive database on Cytochrome P450 enzymes including a tool for analysis of CYP-drug interactions.

(2010) Nucleic Acids Res 38

PubMed: 19934256 | PubMedCentral: PMC2808967 | DOI: 10.1093/nar/gkp970

Overview of the coverage of the CYP-classes with experimentally determined structures CYP PDB-ID 1A2 2hi4 2A6 1z10, 1z11, 1fdu, 2fdv, 2fdw, 2fdy, 2pg5, 2pg6, 2pg7 2A13 2p85 2C8 1pq2, 2nni, 2vn0 2C9 1o... 2, 1og5, 1r9o 2D6 2f9q 2R1 3c6g 3A4 1w0e, 1w0f, 1w0g, 1tqn, 2j0d, 2v0m 8A1 2iag With 1170 drugs and ∼3800 interactions, SuperCYP provides the largest number of CYP relations and corresponding information available online.

Publication Year: 2010


Structure and dynamics of the membrane-bound cytochrome P450 2C9.

(2011) PLoS Comput Biol 7

PubMed: 21852944 | PubMedCentral: PMC3154944 | DOI: 10.1371/journal.pcbi.1002152

The membrane stabilizes open conformations of the internal aromatic gate In the 1R9O crystal structure, the aromatic gate is closed and locks the substrate in the bound position above the heme center ... 25] .

The rmsd between the reference structure and the 1R9O crystal structure varied between 0.8 Å and 1.2 Å and was calculated by superimposing the backbone atoms of residues 47 to 200 and 250 to 492.

We simulated models derived from two conformations of CYP2C9 ( Table 1 ), both based on the flurbiprofen-bound crystal structure (pdb 1R9O) [25] .

Materials and Methods CYP2C9 models We constructed 2 models of soluble CYP2C9 based on the flurbiprofen-bound crystal structure (pdbid 1R9O, 1.9 Å resolution) [25] : (i) 1R9O1 has 2 small helices in the FG loop (F' and G'), and (ii) 1R9O2 has a small β-sheet in the mostly unstructured FG loop and is similar to an unpublished crystal structure of CYP2C9 (Eric Johnson, personal communication).

Publication Year: 2011


Variability in docking success rates due to dataset preparation.

(2012) J Comput Aided Mol Des 26

PubMed: 22566074 | PubMedCentral: PMC3397132 | DOI: 10.1007/s10822-012-9570-1

Table 1 Complexes requiring additional preparation Inconsistent stereo configuration  1GKC 1L7F 1R55 1VCJ  1GM8 1M2Z 1R58 1W1P  1GPK 1MMV 1R9O 1W2G  1HP0 1OF1 1... 19 1X8X  1HVY 1OF6 1S3V 1XM6  1HWI 1OYT 1SQ5 1YGC  1HWW 1P2Y 1SQN 1YQY  1K3U 1P62 1TT1 1YV3  1KE5 1Q1G 1UML 1YWR  1KZK 1R1H 1V0P Co-factors with incorrect number of hydrogens  1G9V 1KZK 1Q1G 1W1P  1HWI 1M2Z 1Q4G 1W2G  1IA1 1MMV 1R9O 1XM6  1J3J 1OPK 1T9B 1XOQ  1JJE 1P62 1TZ8 Alternate locations missing hydrogens  1GM8 1OPK 1T9B 1XOZ  1HNN 1OQ5 1TZ8 1Y6B  1HP0 1Q4G 1UOU 1YV3  1IA1 1R1H 1VCJ 1YWR  1KZK 1S19 1W1P 1Z95  1L2S 1S3V 1X8X 2BR1  1N46 1T46 1XOQ The ‘modified’ ACS-Astex dataset Upon closer examination of some of the complexes it was noted that the hydrogen bond network was not optimal and therefore further optimization was warranted.

Table 2 Complexes requiring capping of chain termini or chain breaks Complexes requiring capping of chain termini  1GKC 1MEH 1Q41 1V48  1GM8 1 MMV 1R55 1V4S  1GPK 1 MZC 1R9O 1W1P  1HNN 1N1M 1S19 1W2G  1HP0 1N2J 1SJ0 1XM6  1HWI 1N2V 1SQN 1XOQ  1HWW 1N46 1T46 1XOZ  1IG3 1OF1 1T9B 1Y6B  1J3J 1OF6 1TT1 1YGC  1JD0 1OPK 1TZ8 1YQY  1JJE 1OQ5 1U1C 1YV3  1JLA 1OYT 1U4D 1YVF  1K3U 1P2Y 1UML 1YWR  1LPZ 1P62 1UNL 2BM2  1LRH 1PMN 1UOU 2BR1  1M2Z 1Q1G 1V0P 2BSM Complexes requiring capping of chain breaks  1GPK 1N46 1SJ0 1V48  1HP0 1NAV 1SQ5 1W2G  1HWI 1OF1 1SQN 1XM6  1J3J 1OF6 1T46 1XOQ  1JLA 1OYT 1T9B 1Y6B  1KE5 1P62 1U1C 1YV3  1L2S 1PMN 1U4D 1YWR  1MEH 1Q41 1UOU 1Z95  1MMV 1R9O 1V0P 2BR1 The ‘corrected’ ACS-Astex dataset After the session transpired at the ACS meeting, 3 structures from the ACS-Astex set (1GPK, 1HVY and 1S3V) were identified as containing an inverted stereocenter in the original dataset given to the participants compared to the original PDB structure.

Publication Year: 2012


Directory of useful decoys, enhanced (DUD-E): better ligands and decoys for better benchmarking.

(2012) J Med Chem 55

PubMed: 22716043 | PubMedCentral: PMC3405771 | DOI: 10.1021/jm300687e

45 Table 2 Overview of Representative Targets target class gene ID description total ligands clustered ligands experimental decoys matched decoys PDB LogAUC (%) ROC EF 1 AUC (%) cytochrome P450 CP2C9 ... ytochrome P450 2C9 145 120 176 7450 1R9O 7 3 60   CP3A4 cytochrome P450 3A4 302 170 267 11800 3NXU 7 2 63   GPCR AA2AR adenosine A2a receptor 3057 482 192 31550 3EML 28 22 83   ADRB1 β-1 adrenergic receptor 648 247 69 15850 2VT4 19 11 76   CXCR4 C-X-C chemokine receptor type 4 40 40 14 3406 3ODU 36 18 90   ion channel GRIA2 glutamate receptor ionotropic AMPA 2 476 158 201 11845 3KGC 23 23 71   GRIK1 glutamate receptor ionotropic kainate 1 136 101 235 6550 1VSO 35 27 86   kinase AKT1 serine/threonine-protein kinase AKT 585 293 53 16450 3CQW 27 29 72   MK10 c-Jun N-terminal kinase 3 199 104 23 6600 2ZDT 24 11 82   MK14 MAP kinase p38 α 2205 578 73 35850 2QD9 17 10 74   miscellaneous KIF11 kinesin-like protein 1 272 116 29 6850 3CJO 34 35 77   XIAP inhibitor of apoptosis protein 3 100 100 7 5150 3HL5 52 55 88   nuclear receptor ESR1 estrogen receptor α 1297 383 136 20685 1SJ0 18 15 67   MCR mineralocorticoid receptor 201 94 2 5150 2AA2 –4 2 36   THB thyroid hormone receptor β-1 246 103 29 7450 1Q4X 36 38 79   PPARD peroxisome proliferator-activated receptor δ 699 240 79 12250 2ZNP 32 20 89   other enzymes FNTA protein farnesyltransferase type I α 1430 592 132 51500 3E37 16 7 76   HDAC8 histone deacetylase 8 309 170 73 10450 3F07 29 24 80   HIVINT HIV type 1 integrase 167 100 268 6650 3NF7 8 2 64   KITH thymidine kinase 57 57 68 2850 2B8T 15 0 80   PARP1 poly (ADP-ribose)polymerase-1 1031 508 12 30050 3L3M 25 21 79   PUR2 GAR transformylase 50 50 12 2700 1NJS 51 50 92   protease DPP4 dipeptidyl peptidase IV 1939 533 167 40950 2I78 41 41 87   FA10 coagulation factor X 3090 537 176 28325 3KL6 39 36 87   LKHA4 leukotriene A4 hydrolase 343 171 21 9450 3CHP 18 4 82   MMP13 matrix metallo-proteinase 13 1632 572 26 37200 830C 12 5 71 To increase scaffold diversity and to make smaller, more manageable ligand sets, we clustered the raw ChEMBL ligands by their Bemis–Murcko atomic frameworks.

Publication Year: 2012


Quantum mechanics/molecular mechanics modeling of regioselectivity of drug metabolism in cytochrome P450 2C9.

(2013) J Am Chem Soc 135

PubMed: 23641937 | PubMedCentral: PMC3670427 | DOI: 10.1021/ja402016p

Asn204 formed a hydrogen bond to the acid group of flurbiprofen in the 1R9O crystal structure (the starting point for the calculations in this work).

31 There are significant differences between the 1R9O and 1OG5 crystal structures, most notably the conformation of the Arg108 side chain, which points in toward the active site in 1R9O, and hydrogen-bonds to the carboxylic acid group of flurbiprofen.

Publication Year: 2013


Distal effect of amino acid substitutions in CYP2C9 polymorphic variants causes differences in interatomic interactions against (S)-warfarin.

(2013) PLoS One 8

PubMed: 24023924 | PubMedCentral: PMC3759441 | DOI: 10.1371/journal.pone.0074053

This docked structure with ( S )-warfarin in complex with CYP2C9 is similar to that of flurbiprofen-bound CYP2C9 crystal structure (PDB ID: 1R9O [35] ).

Publication Year: 2013


Identifying cytochrome p450 functional networks and their allosteric regulatory elements.

(2013) PLoS One 8

PubMed: 24312617 | PubMedCentral: PMC3849357 | DOI: 10.1371/journal.pone.0081980

Each residue network was further mapped to the atomic structure of CYP2C9 (PDB code 1R9O) in B -E and shown in the following different orientations: the membrane-binding network ( B ), the catalytic n... twork ( C ), the dimerization network ( D ), and the heme-binding network ( E ).

Residues identified as belonging to membrane-binding networks were mapped to the molecular structures of CYP1A (PDB code 2HI4; A ), CYP2C (PDB code 1R9O; B ), CYP3A (PDB code 1W0E; C ), and CYP2D (PDB code 2F9Q; D ).

The structures of CYP3A4, CYP1A2, CYP2C9, and CYP2D6 were abstracted from the crystal structures (PDB code 1W0E [ 39 ], 2HI4 [ 40 ], 1R9O [ 41 ], and 2F9Q [ 42 ], respectively).

Dimerization and membrane-binding networks were mapped on the crystal structure model of a CYP2C9 dimer (PDB code 1R9O).

Residues identified as belonging to heme-binding networks were mapped to the molecular structures of CYP1A (PDB code 2HI4; A ), CYP2C (PDB code 1R9O; B ), CYP3A (PDB code 1W0E; C ), and CYP2D (PDB code 2F9Q; D ).

Publication Year: 2013


Study on incompatibility of traditional chinese medicine: evidence from formula network, chemical space, and metabolism room.

(2013) Evid Based Complement Alternat Med 2013

PubMed: 24369478 | PubMedCentral: PMC3858019 | DOI: 10.1155/2013/352145

The crystal structures of these enzymes were collected from PDB, with the names and their PDB code as follows: CYP 1A1 (PDB code: 4I8V), CYP 1A2 (PDB code: 2HI4), CYP 1B1 (PDB code: 3PM0), CYP 2A6 (PD... code: 1Z10), CYP 2A13 (PDB code: 2PB5), CYP 2B4 (PDB code: 3TMZ), CYP 2B6 (PDB code: 3UA5), CYP 2C5 (PDB code: 1NR6), CYP 2C8 (PDB code: 2VN0), CYP 2C9 (PDB code: 1R9O), CYP 2C18 (PDB code: 2H6P), CYP 2C19 (PDB code: 4GQS), CYP 2D6 (PDB code: 3TDA), CYP 2E1 (PDB code: 3T3Z), and CYP 3A4 (PDB code: 3NXU).

Publication Year: 2013


Automating crystallographic structure solution and refinement of protein-ligand complexes.

(2014) Acta Crystallogr D Biol Crystallogr 70

PubMed: 24419387 | PubMedCentral: PMC3919266 | DOI: 10.1107/S139900471302748X

In PDB entry 1r9o , for instance, the search model (PDB entry 1n6b ) has only 76% sequence identity and although ligand placement was successful, there are large regions on the surface of the protein ... hat have undergone significant conformational changes and require rebuilding or deletion.

(i) 21 (58%) of the structures (PDB entries 1br6 , 1b9v , 1exa , 1fcx , 1fcz , 1hq2 , 1hwi , 1k3u , 1ml1 , 1n2j , 1of1 , 1of6 , 1pmn , 1q1g , 1q41 , 1r9o , 1tt1 , 1w1p , 1w2g , 1yv3 and 2br1 ) worked unambiguously with default settings and without intervention; manual inspection confirmed that the ligand placement was essentially correct, with only minor disagreements with the published model (if any).

PDB code Re-refined R work / R free Pipeline R work / R free Placed/present Ligand r.m.s.d.(s) (Å) 1b9v 0.175/0.202 0.200/0.224 1/1 0.65 1br6 0.180/0.224 0.192/0.225 1/1 0.20 1cx2 0.245/0.308 0.250/0.362 0/4 — 1exa 0.169/0.192 0.182/0.213 1/1 0.06 1fcx 0.135/0.167 0.152/0.181 1/1 0.13 1fcz 0.141/0.175 0.157/0.182 1/1 0.08 1fjs 0.158/0.204 0.231/0.255 0/1 — 0.178/0.208 1/1 C 0.59 1g9v 0.141/0.166 0.135/0.171 1/2 0.17 0.136/0.171 2/2 C 0.16, 0.17 1hp0 0.163/0.216 0.173/0.227 2/2 P 0.31, 2.04 1hq2 0.121/0.160 0.134/0.166 1/1 0.10 1hwi 0.165/0.189 0.177/0.198 4/4 0.32–0.44 1hww 0.136/0.167 0.222/0.248 0/1 — 1k3u 0.135/0.162 0.137/0.165 1/1 0.05 1l2s 0.147/0.168 0.168/0.195 2/3 0.15, 0.16 1ml1 0.159/0.208 0.173/0.208 6/6 0.25–0.86 1mq6 0.171/0.221 0.184/0.227 1/1 P 1.36 0.179/0.230 1/1 C 0.68 1mzc 0.146/0.168 0.152/0.168 1/1 P 2.51 1n2j 0.168/0.193 0.185/0.210 2/2 0.10, 0.25 1of1 0.156/0.179 0.175/0.197 2/2 0.11, 0.13 1of6 0.173/0.191 0.208/0.230 8/8 0.11–1.82 1oq5 0.120/0.164 0.231/0.264 0/1 — 0.148/0.188 1/1 C 0.86 1pmn 0.190/0.224 0.218/0.249 1/1 0.53 1q1g 0.156/0.185 0.195/0.214 6/6 0.18–0.63 1q41 0.182/0.195 0.207/0.222 2/2 0.19, 0.30 1qhi 0.214/0.253 0.348/0.403 0/1 — 1r9o 0.162/0.193 0.240/0.284 1/1 0.39 1tt1 0.147/0.171 0.158/0.182 2/2 0.17, 0.19 1u4d 0.187/0.206 0.200/0.219 2/2 P 0.64, 0.67 1unl 0.190/0.214 0.264/0.291 0/1 — 0.246/0.276 1/1 C 0.98 1w1p 0.196/0.230 0.225/0.257 2/2 0.22, 0.30 1w2g 0.177/0.198 0.204/0.221 2/2 0.26, 0.56 1yqy 0.201/0.246 0.351/0.411 0/1 — 1yv3 0.151/0.184 0.169/0.193 1/1 0.19 2ack 0.159/0.185 0.446/0.507 — — 0.165/0.193 1/1 C 0.42 2br1 0.162/0.195 0.170/0.212 1/1 0.33 4cox 0.205/0.30 0.256/0.361 0/4 —

Publication Year: 2014