Primary Citation PubMed: 14676196
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Construction of 3D models of the CYP11B family as a tool to predict ligand binding characteristics.
(2007) J Comput Aided Mol Des 21
PubMed: 17646925 | PubMedCentral: PMC2039848 | DOI: 10.1007/s10822-007-9128-9
Species information: Pseudomonas-Putida 2CPP, Bacillus Megaterium 1BU7, Saccharopolyspora-Erythreaea 1JIN, Pseudomonas -SP 1CPT, Archaeon Sulfolobus Solfataricus 1F4U, Fusarium-Oxysporum 1ROM, Mycobac... erium Tuberculosis 1EA1, Oryctolagus Cuniculus 1SUO and 1NR6, Homo Sapiens 1PQ2, 1OG2, 1W0E and 2F9Q Because of the low sequence identity of the CYP11B family, we have chosen to create a hybrid template for hCYP11B2 using MOE-Homology [ 42 ], constructed from the crystal structures of CYP101 (pdb code: 2CPP) and CYP2C5 (pdb code: 1NR6).
Publication Year: 2007
Use of complementary cation and anion heavy-atom salt derivatives to solve the structure of cytochrome P450 46A1.
(2008) Acta Crystallogr D Biol Crystallogr 64
PubMed: 18453684 | PubMedCentral: PMC2467524 | DOI: 10.1107/S0907444908004046
Homology models for molecular-replacement searches were created using Swiss-Model (Schwede et al. , 2003 ▶ ) based on CYP3A4 (PDB code 1tqn ; Yano et al. , 2004 ▶ ) and CYP2C8 (PDB cod... 1pq2 ; Schoch et al. , 2004 ▶ ).
Publication Year: 2008
Genome-wide identification and characterization of cytochrome P450 monooxygenase genes in the ciliate Tetrahymena thermophila.
(2009) BMC Genomics 10
PubMed: 19409101 | PubMedCentral: PMC2691746 | DOI: 10.1186/1471-2164-10-208
Previously reported P450 protein crystal structure data were downloaded from the RCSB (Brookhaven protein data bank) website , including P450cam (CYP101), P450BM3 (CYP102), P450terp (CYP108) and P450e... yF (CYP107A1) from bacteria, P450nor (CYP55A1) from fungi, CYP2C5, CYP2C8 and CYP3A4 from mammals, corresponding to PDB codes 1UTU, 1ZO4, 1CPT, 1EUP, 1EHE, 1NR6, 1PQ2 and 1TQN, respectively.
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
Prediction and analysis of the modular structure of cytochrome P450 monooxygenases.
(2010) BMC Struct Biol 10
PubMed: 20950472 | PubMedCentral: PMC3224734 | DOI: 10.1186/1472-6807-10-34
CYP PDB entry Resolution [Å] Ligand Organism Class II CYPs (CPR-type) 1A2 2HI4 1.95 + Homo sapiens 2A6 1Z10 1.90 + Homo sapiens 2A13 2P85 2.35 + Homo sapiens 2B4 1SUO 1.90 + Oryctolagus cunicu... us 2C5 1N6B 2.30 + Oryctolagus cuniculus 2C8 1PQ2 2.70 + Homo sapiens 2C9 1OG2 2.60 + Homo sapiens 2D6 2F9Q 3.00 - Homo sapiens 2R1 2OJD 2.80 + Homo sapiens 3A4 1TQN 2.05 - Homo sapiens 102A1 1BU7 1.65 - Bacillus megaterium (P450 BM-3) 175A1 1N97 1.80 - Thermus thermophilus Class I CYPs 51B1 1E9X 2.10 + Mycobacterium tuberculosis 101D 2CPP 1.63 + Pseudomonas putida (P450cam) 107A1 1OXA 2.10 + Saccharopolyspora erythrea 107L1 2BVJ 2.10 - Streptomyces venezuelae 108A 1CPT 2.30 - Pseudomonas sp .
Table 2 Positions which correspond to F87 in P450 BM-3 and predicted position, and prediction of positions in new structures CYP PDB-Code Position in crystal structure Predicted position 8A 2IAG - - 51B1 1E9X - V88 55A2 1CL6 V87 V87 101D 2CPP T101 I99 107A1 1OXA G91 G91 107L1 2BVJ L93 L93 108A 1CPT T103 T103 119 1IO7 L69 L69 152A1 1IZO Q85 Q85 154A1 1ODO F88 F88 154C1 1GWI L93 L93 158A1 2DKK A97 S95 158A2 1S1F G94 G94 165B3 1LFK M89 N87 165C4 1UED S98 S98 167A1 1Q5D F96 G94 175A1 1N97 L80 L80 176A1 1T2B A91 M89 199A2 2FR7 L100 L100 245A1 2Z3T V99 V99 1A2 2HI4 T124 S126 2A6 1Z10 V117 V117 2A13 2P85 A117 A117 2B4 1SUO I114 I114 2C5 1N6B A113 A113 2C8 1PQ2 I113 I113 2C9 1OG2 V113 V113 2D6 2F9Q F120 F120 2R1 2OJD L125 L125 3A4 1TQN S119 S119 102A1 1BU7 (reference) F87 F87 2E1 3E4E I94 I94 3A43 2V0M S119 S119 7A1 2DAX - D98 19A1 3EQM F134 F134 46A1 2Q9F V126 S127 74A1 2RCH S128 L127 105A1 2ZBX I96 I96 105K1 2Z36 L96 L96 120A1 2VE3 A94 A94 231A2 2RFB I48 I48 248A 3BUJ L80 L80 To validate our structure-based method to assign SCRs in a one-leave-out cross-validation, the position which corresponds to F87 in CYP102A1 was predicted for each sequence of each structure.
Homology modeling of mosquito cytochrome P450 enzymes involved in pyrethroid metabolism: insights into differences in substrate selectivity.
(2011) BMC Res Notes 4
PubMed: 21892968 | PubMedCentral: PMC3228512 | DOI: 10.1186/1756-0500-4-321
Crystal structures of ligand-free CYP3A4 (PDB: 1TQN ) [ 10 ], CYP2C8 (PDB: 1PQ2 ) [ 11 ], and CYP2C9 (PDB: 1OG2 ) [ 12 ] were used as templates since their sequences were most similar to the target P4... 0s (14-33% primary sequence identity).
Publication Year: 2011
PubMed ID is not available.
Published in 2015
CYP638B18 was modeled following the same protocol and using crystal structures of two human drug-metabolizing cytochromes as templates (PDB IDs: 1Z10 and 1PQ2).
Publication Year: 2015
The template structure for this model was CYP2C8 [PDB:1PQ2].
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