Citations in PubMed

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PDB ID Mentions in PubMed Central Article count: 9

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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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


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


Does compound I vary significantly between isoforms of cytochrome P450?

(2011) J Am Chem Soc 133

PubMed: 21863858 | PubMedCentral: PMC3180200 | DOI: 10.1021/ja203157u

The simulation originating from the 1OG2 crystal structure in the absence of substrate will be referred to as 2C9_apo .

Two crystal structures, both obtained by Williams et al.,( 43 ) were used for the calculations on CYP2C9; the 1OG2 structure was used for simulating CYP2C9 in the absence of substrate, while the 1OG5 structure was used for all simulations containing the substrate S -warfarin.

Publication Year: 2011


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

(A) Comparison of the BC-loops of P450 BM-3 [PDB: 1BU7] in beige, CYP2C9 [PDB: 1OG2] in green, CYP154C1 [PDB: 1GWI] in pink, CYP101D [PDB: 2CPP] in yellow and CYP107A1 [PDB: 1OXA] in blue.

The CPR-type FMN/FAD from Rattus norvegicus [PDB: 3ES9 ] is shown in yellow, the parts of the P450 domain of CYP2C9 from Homo sapiens [PDB: 1OG2 ] are shown in grey and green for CYP101D from Pseudomonas putida [PDB: 2CPP ], respectively.

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 cuniculus 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.

The visualization of the reductase interaction sites RIS1 and RIS2 was generated by the superposition of the FMN-domains of CYP102A1 [PDB: 1BVY ] and the CPR-type FMN/FAD reductase from Rattus norvegicus [PDB: 3ES9 ] and the superposition of the P450-domains of CYP2C9 from Homo sapiens [PDB: 1OG2 ] CYP101D and from Pseudomonas putida [PDB: 2CPP ] on the P450-domain of CYP102A1.

Publication Year: 2010


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).

Template sequences of CYP3A4 (1TQN chain A), CYP2C9 (1OG2 chain A) and CYP2C8 (1PQN chain A) are aligned against target sequences CYP6AA3, CYP6P7 and CYP6P8.

Publication Year: 2011


Membrane position of ibuprofen agrees with suggested access path entrance to cytochrome P450 2C9 active site.

(2011) J Phys Chem A 115

PubMed: 21744854 | PubMedCentral: PMC3257864 | DOI: 10.1021/jp204488j

Results Model Building The N-terminal sequence missing from the initial X-ray structure PDB ID 1OG2( 29 ) was modeled as an α-helix.

5 The X-ray structure of 1OG2 indicates the possible active site access paths, the solvent channel and the 2c channel (between the B′ and G helices).

Right panel shows RMSF per residue for simulations of wt CYP2C9 in membrane (black line), wt CYP2C9 in water (green line), CYP2C9 based on crystal structure 1OG2 (without N-terminal anchor) in water (red line), as well as RMSF calculated from the B-factors of crystals structures 1OG2 and 1OG5 (cyan and blue lines, respectively).

Materials and Methods Protein Model Building We used the crystal structure of ligand-free CYP2C9 (PDB ID 1OG2) as a template for model building.

Effects of the Membrane on the CYP Structure and Flexibility The RMSF profile calculated from the simulation of CYP2C9 based on 1OG2 X-ray structure agrees well with published results and displays the previously identified common flexible regions.

If the transmembrane segment is not present ( 1OG2 ), the prediction incorrectly exposes residues around the N-terminus to the solvent (Figure 5 , blue).

Publication Year: 2011


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

The 1OG2 and 1OG5 structures correspond to the apo form and a complex containing S -warfarin, respectively.

Publication Year: 2013


Ensemble generation and the influence of protein flexibility on geometric tunnel prediction in cytochrome P450 enzymes.

(2014) PLoS One 9

PubMed: 24956479 | PubMedCentral: PMC4067289 | DOI: 10.1371/journal.pone.0099408

Methods MD Simulations High resolution CYP crystal structures where both the apo and holo forms were available were selected for this study; CYP119 (apo: 1IO9, resolution 2.05 Å and holo: 1F4T... resolution 1.93 Å), CYP2C9 (apo: 1OG2, resolution 2.60 Å and holo: 1OG5, resolution 2.55 Å), and CYP3A4 (apo: 4I3Q, resolution 2.60 Å and holo: 3UA1, resolution 2.15 Å).

Publication Year: 2014


Estimation of the binding modes with important human cytochrome P450 enzymes, drug interaction potential, pharmacokinetics, and hepatotoxicity of ginger components using molecular docking, computational, and pharmacokinetic modeling studies.

(2015) Drug Des Devel Ther 9

PubMed: 25733806 | PubMedCentral: PMC4338259 | DOI: 10.2147/DDDT.S74669

16 – 18 Briefly, the crystal structures of human CYP1A2 (protein data bank [PDB] code 2HI4), 2C9 CYP2C9 (PDB code 1OG2), 2C19 (PDB code 4GQS), 2D6 (PDB code 2F9Q), and 3A4 (PDB code 1W0F) were... obtained from the Protein Data Bank ( http://www.rcsb.org/pdb/ ).

Figure 3 Binding modes of ginger main active components in human CYP2C9 (PDB code 1OG2).

Table 1 Interacting forces of main active components of ginger with human CYP1A2, 2C9, 2D6, 2C19, and 3A4 Compound CDCOKER interaction energy (CIE kcal/mol) H-bond number Residues involved in H-bond formation Charge interaction Residues involved in charge interaction π–π stacking Residues involved in π–π stacking CYP1A2 (PDB ID: 2HI4) 6-Gingerol 55.9802 0 / 0 / 0 / 8-Gingerol 60.0329 0 / 0 / 0 / 10-Gingerol 61.3568 1 H-Gly316 0 / 0 / 6-Shogaol 55.9354 0 / 0 / 1 Phe260 8-Shogaol 58.6712 0 / 0 / 1 Phe260 10-Shogaol 56.4091 0 / 0 / 0 / Ar-Curcumene 36.2667 0 / 0 / 0 / β-Bisabolene 35.991 0 / 0 / 0 / β-Sesquiphelandrene 31.8433 0 / 0 / 0 / 6-Gingerdione 59.0853 0 / 0 / 2 Phe226 Phe260 (−)-Zingiberene 36.363 0 / 0 / 0 / Methyl-6-isogingerol 51.232 1 H-Gly316 0 / 1 Phe226 CYP2C9 (PDB ID: 1OG2) 6-Gingerol 38.3346 3 H-Leu208 O-Gln214 O-Asn217 0 / 0 / 8-Gingerol 41.0866 1 H-Leu208 0 / 0 / 10-Gingerol 45.8869 1 H-Leu208 0 / 0 / 6-Shogaol 38.4989 2 H-Thr301 O-Thr301 0 / 0 / 8-Shogaol 40.3159 0 / 0 / 0 / 10-Shogaol 45.2874 0 / 0 / 0 / Ar-Curcumene 27.0167 0 / 0 / 0 / β-Bisabolene 24.3503 0 / 0 / 0 / β-Sesquiphelandrene 24.6193 0 / 0 / 0 / 6-Gingerdione 38.5734 1 O-Asn107 0 / 0 / (−)-Zingiberene 25.4757 0 / 0 / 0 / Methyl-6-isogingerol 39.2082 1 H-Asp293 0 / 0 / CYP2C19 (PDB ID: 4GQS) 6-Gingerol 30.5894 1 H-Gly296 0 / 0 / 8-Gingerol 34.7882 1 O-Asn204 0 / 0 / 10-Gingerol 41.7354 0 / 0 / 0 / 6-Shogaol 31.298 1 O-Gln214 0 / 0 / 8-Shogaol 37.7374 1 O-Asn218 0 / 0 / 10-Shogaol 42.1221 0 / 0 / 0 / Ar-Curcumene 26.7476 0 / 0 / 0 / β-Bisabolene 24.9395 0 / 0 / 0 / β-Sesquiphelandrene 25.8704 0 / 0 / 0 / 6-Gingerdione 33.6531 0 / 0 / 0 / (−)-Zingiberene 23.3969 0 / 0 / 0 / Methyl-6-isogingerol 30.036 2 H-Gln214 O-Asn217 0 / 0 / CYP2D6 (PDB ID: 2F9Q) 6-Gingerol 49.7194 4 H-Arg441 O-His376 O-Arg101 O-Arg101 0 / 0 / 8-Gingerol 55.2159 4 H-Arg441 O-Arg101 O-Arg101 O-His376 0 / 0 / 10-Gingerol 57.6051 3 H-Arg441 O-Arg10 O-Arg101 0 / 0 / 6-Shogaol 46.6251 3 H-Arg441 O-Arg 101 O-His376 0 / 0 / 8-Shogaol 52.6567 3 H-Arg441 O-Arg101 O-His376 0 / 0 / 10-Shogaol 56.3996 3 O-His376 O-Arg101 O-Arg101 0 / 0 / Ar-Curcumene 29.9457 0 / 0 / 0 / β-Bisabolene 30.5663 0 / 0 / 0 / β-Sesquiphelandrene 28.6495 0 / 0 / 0 / 6-Gingerdione 50.0314 4 H-Arg441 O-Arg101 O-Arg101 O-His376 0 / 0 / (−)-Zingiberene 29.6369 0 / 0 / 0 / Methyl-6-isogingerol 51.8517 1 O-Arg101 0 / 0 / CYP3A4 (PDB ID: 1W0F) 6-Gingerol 51.1796 2 H-Ala305 H-Glu374 0 / 0 / 8-Gingerol 53.5899 2 H-Ala305 H-Glu374 0 / 0 / 10-Gingerol 54.8047 1 H-Glu374 0 / 0 / 6-Shogaol 49.1685 1 H-Ala305 0 / 0 / 8-Shogaol 53.9844 1 H-Ala305 0 / 0 / 10-Shogaol 63.0781 1 H-Ala305 0 / 0 / Ar-Curcumene 28.8825 0 / 0 / 0 / β-Bisabolene 27.4614 0 / 0 / 0 / β-Sesquiphelandrene 26.3732 0 / 0 / 0 / 6-Gingerdione 52.9237 2 H-Ala305 O-Arg105 0 / 0 / (−)-Zingiberene 27.9257 0 / 0 / 0 / Methyl-6-isogingerol 47.7586 0 / 0 / 0 / Abbreviation: CYP, cytochrome P450.

Publication Year: 2015