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PDBsum entry 2j0d

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Oxidoreductase PDB id
2j0d
Jmol
Contents
Protein chain
446 a.a. *
Ligands
HEM ×2
ERY
Waters ×49
* Residue conservation analysis
PDB id:
2j0d
Name: Oxidoreductase
Title: Crystal structure of human p450 3a4 in complex with erythromycin
Structure: Cytochrome p450 3a4. Chain: a, b. Fragment: soluble domain, residues 24-502. Synonym: quinine 3-monooxygenase, cypiiia4, nifedipine oxidase, taurochenodeoxycholate 6-alpha-hydroxylase, nf-25, p450-pcn1. Ec: 1.14.14.1, 1.14.13.67, 1.14.13.97. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Organ: liver. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.75Å     R-factor:   0.242     R-free:   0.315
Authors: T.Sjogren,M.Ekroos
Key ref:
M.Ekroos and T.Sjögren (2006). Structural basis for ligand promiscuity in cytochrome P450 3A4. Proc Natl Acad Sci U S A, 103, 13682-13687. PubMed id: 16954191 DOI: 10.1073/pnas.0603236103
Date:
02-Aug-06     Release date:   04-Sep-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P08684  (CP3A4_HUMAN) -  Cytochrome P450 3A4
Seq:
Struc:
503 a.a.
446 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   7 terms 
  Biological process     lipid metabolic process   16 terms 
  Biochemical function     oxidoreductase activity     18 terms  

 

 
DOI no: 10.1073/pnas.0603236103 Proc Natl Acad Sci U S A 103:13682-13687 (2006)
PubMed id: 16954191  
 
 
Structural basis for ligand promiscuity in cytochrome P450 3A4.
M.Ekroos, T.Sjögren.
 
  ABSTRACT  
 
Cytochrome P450 (CYP) 3A4 is the most promiscuous of the human CYP enzymes and contributes to the metabolism of approximately 50% of marketed drugs. It is also the isoform most often involved in unwanted drug-drug interactions. A better understanding of the molecular mechanisms governing CYP3A4-ligand interaction therefore would be of great importance to any drug discovery effort. Here, we present crystal structures of human CYP3A4 in complex with two well characterized drugs: ketoconazole and erythromycin. In contrast to previous reports, the protein undergoes dramatic conformational changes upon ligand binding with an increase in the active site volume by >80%. The structures represent two distinct open conformations of CYP3A4 because ketoconazole and erythromycin induce different types of coordinate shifts. The binding of two molecules of ketoconazole to the CYP3A4 active site and the clear indication of multiple binding modes for erythromycin has implications for the interpretation of the atypical kinetic data often displayed by CYP3A4. The extreme flexibility revealed by the present structures also challenges any attempt to apply computational design tools without the support of relevant experimental data.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Chemical structures of ketoconazole (A) and erythromycin (B).
Figure 3.
Fig. 3. Ketoconazole binding to CYP3A4. Ketoconazole molecules are shown in orange stick representation. The heme group is shown in magenta. Secondary structure and stick representations of side chains within 4 Å from the ligands are shown in green. The C-terminal loop (residues 464–498) was omitted for clarity. A superposition of the ligand-free structure (Protein Data Bank ID code 1TQN) is shown in gray. The mesh represents a F[o] – F[c] difference map contoured at 4.5 calculated in the absence of ligands by using the program AutoBUSTER (19).
 
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  21143007 H.Fernando, J.A.Rumfeldt, N.Y.Davydova, J.R.Halpert, and D.R.Davydov (2011).
Multiple substrate-binding sites are retained in cytochrome P450 3A4 mutants with decreased cooperativity.
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20863320 M.Yao, M.Dai, Z.Liu, L.Huang, D.Chen, Y.Wang, D.Peng, X.Wang, Z.Liu, and Z.Yuan (2011).
Comparison of the substrate kinetics of pig CYP3A29 with pig liver microsomes and human CYP3A4.
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21429746 R.Aspiotis, A.Chen, E.Cauchon, D.Dubé, J.P.Falgueyret, S.Gagné, M.Gallant, E.L.Grimm, R.Houle, H.Juteau, P.Lacombe, S.Laliberté, J.F.Lévesque, D.MacDonald, D.McKay, M.D.Percival, P.Roy, S.M.Soisson, and T.Wu (2011).
The discovery and synthesis of potent zwitterionic inhibitors of renin.
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Minor modifications of the C-terminal helix reschedule the favored chemical reactions catalyzed by theta class glutathione transferase T1-1.
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20387782 D.Fishelovitch, S.Shaik, H.J.Wolfson, and R.Nussinov (2010).
How does the reductase help to regulate the catalytic cycle of cytochrome P450 3A4 using the conserved water channel?
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Crystal structures of Trypanosoma brucei sterol 14alpha-demethylase and implications for selective treatment of human infections.
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PDB codes: 3g1q 3gw9
19878193 H.Sun, and D.O.Scott (2010).
Structure-based drug metabolism predictions for drug design.
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20580544 H.Wade (2010).
MD recognition by MDR gene regulators.
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20937904 I.F.Sevrioukova, and T.L.Poulos (2010).
Structure and mechanism of the complex between cytochrome P4503A4 and ritonavir.
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PDB code: 3nxu
19944064 J.C.Talakad, P.R.Wilderman, D.R.Davydov, S.Kumar, and J.R.Halpert (2010).
Rational engineering of cytochromes P450 2B6 and 2B11 for enhanced stability: Insights into structural importance of residue 334.
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20097757 J.N.Lampe, R.Brandman, S.Sivaramakrishnan, and P.R.de Montellano (2010).
Two-dimensional NMR and all-atom molecular dynamics of cytochrome P450 CYP119 reveal hidden conformational substates.
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21170327 J.Yan, and Z.Cai (2010).
Molecular evolution and functional divergence of the cytochrome P450 3 (CYP3) Family in Actinopterygii (ray-finned fish).
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20673214 K.N.Myasoedova, and K.N.Timofeev (2010).
Conformational changes near the cytochrome P450 active site upon binding of two different ligands.
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19727863 N.Krishnamoorthy, P.Gajendrarao, S.Thangapandian, Y.Lee, and K.W.Lee (2010).
Probing possible egress channels for multiple ligands in human CYP3A4: a molecular modeling study.
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20579289 N.Osada, Y.Uno, K.Mineta, Y.Kameoka, I.Takahashi, and K.Terao (2010).
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20814717 R.Didziapetris, J.Dapkunas, A.Sazonovas, and P.Japertas (2010).
Trainable structure-activity relationship model for virtual screening of CYP3A4 inhibition.
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20583201 R.T.Jones, S.E.Bakker, D.Stone, S.N.Shuttleworth, S.Boundy, C.McCart, P.J.Daborn, R.H.ffrench-Constant, and J.M.van den Elsen (2010).
Homology modelling of Drosophila cytochrome P450 enzymes associated with insecticide resistance.
  Pest Manag Sci, 66, 1106-1115.  
20446763 T.C.Pochapsky, S.Kazanis, and M.Dang (2010).
Conformational plasticity and structure/function relationships in cytochromes P450.
  Antioxid Redox Signal, 13, 1273-1296.  
20697309 V.Agrawal, J.H.Choi, K.M.Giacomini, and W.L.Miller (2010).
Substrate-specific modulation of CYP3A4 activity by genetic variants of cytochrome P450 oxidoreductase.
  Pharmacogenet Genomics, 20, 611-618.  
20879989 Y.Farooq, and G.C.Roberts (2010).
Kinetics of electron transfer between NADPH-cytochrome P450 reductase and cytochrome P450 3A4.
  Biochem J, 432, 485-493.  
19179341 A.Nayeem, S.J.Chiang, S.W.Liu, Y.Sun, L.You, and J.Basch (2009).
Engineering enzymes for improved catalytic efficiency: a computational study of site mutagenesis in epothilone-B hydroxylase.
  Protein Eng Des Sel, 22, 257-266.  
19661995 C.D.Sohl, Q.Cheng, and F.P.Guengerich (2009).
Chromatographic assays of drug oxidation by human cytochrome P450 3A4.
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19856963 C.H.Ngan, D.Beglov, A.N.Rudnitskaya, D.Kozakov, D.J.Waxman, and S.Vajda (2009).
The structural basis of pregnane X receptor binding promiscuity.
  Biochemistry, 48, 11572-11581.  
19728720 D.Fishelovitch, S.Shaik, H.J.Wolfson, and R.Nussinov (2009).
Theoretical characterization of substrate access/exit channels in the human cytochrome P450 3A4 enzyme: involvement of phenylalanine residues in the gating mechanism.
  J Phys Chem B, 113, 13018-13025.  
19605359 H.Zhang, C.Kenaan, D.Hamdane, G.H.Hoa, and P.F.Hollenberg (2009).
Effect of conformational dynamics on substrate recognition and specificity as probed by the introduction of a de novo disulfide bond into cytochrome P450 2B1.
  J Biol Chem, 284, 25678-25686.  
19555717 I.G.Denisov, D.J.Frank, and S.G.Sligar (2009).
Cooperative properties of cytochromes P450.
  Pharmacol Ther, 124, 151-167.  
19204698 I.Nobeli, A.D.Favia, and J.M.Thornton (2009).
Protein promiscuity and its implications for biotechnology.
  Nat Biotechnol, 27, 157-167.  
19937844 J.Dapkunas, A.Sazonovas, and P.Japertas (2009).
Probabilistic prediction of the human CYP3A4 and CYP2D6 metabolism sites.
  Chem Biodivers, 6, 2101-2106.  
19104915 M.K.Leong, Y.M.Chen, H.B.Chen, and P.H.Chen (2009).
Development of a New Predictive Model for Interactions with Human Cytochrome P450 2A6 Using Pharmacophore Ensemble/Support Vector Machine (PhE/SVM) Approach.
  Pharm Res, 26, 987.  
19397311 S.C.Gay, L.Sun, K.Maekawa, J.R.Halpert, and C.D.Stout (2009).
Crystal structures of cytochrome P450 2B4 in complex with the inhibitor 1-biphenyl-4-methyl-1H-imidazole: ligand-induced structural response through alpha-helical repositioning.
  Biochemistry, 48, 4762-4771.
PDB codes: 3g5n 3g93
18395506 A.Nath, C.Fernández, J.N.Lampe, and W.M.Atkins (2008).
Spectral resolution of a second binding site for Nile Red on cytochrome P4503A4.
  Arch Biochem Biophys, 474, 198-204.  
18058908 B.Gorelik, and A.Goldblum (2008).
High quality binding modes in docking ligands to proteins.
  Proteins, 71, 1373-1386.  
19040328 D.R.Davydov, and J.R.Halpert (2008).
Allosteric P450 mechanisms: multiple binding sites, multiple conformers or both?
  Expert Opin Drug Metab Toxicol, 4, 1523-1535.  
18622598 E.M.Isin, and F.P.Guengerich (2008).
Substrate binding to cytochromes P450.
  Anal Bioanal Chem, 392, 1019-1030.  
18484912 E.Stjernschantz, N.P.Vermeulen, and C.Oostenbrink (2008).
Computational prediction of drug binding and rationalisation of selectivity towards cytochromes P450.
  Expert Opin Drug Metab Toxicol, 4, 513-527.  
18393395 E.Yaffe, D.Fishelovitch, H.J.Wolfson, D.Halperin, and R.Nussinov (2008).
MolAxis: efficient and accurate identification of channels in macromolecules.
  Proteins, 73, 72-86.  
18413310 G.A.Schoch, J.K.Yano, S.Sansen, P.M.Dansette, C.D.Stout, and E.F.Johnson (2008).
Determinants of cytochrome P450 2C8 substrate binding: structures of complexes with montelukast, troglitazone, felodipine, and 9-cis-retinoic acid.
  J Biol Chem, 283, 17227-17237.
PDB codes: 2nnh 2nni 2nnj 2vn0
18606741 G.Tai, L.J.Dickmann, N.Matovic, J.J.DeVoss, E.M.Gillam, and A.E.Rettie (2008).
Re-engineering of CYP2C9 to probe acid-base substrate selectivity.
  Drug Metab Dispos, 36, 1992-1997.  
18089574 H.Ouellet, L.M.Podust, and P.R.de Montellano (2008).
Mycobacterium tuberculosis CYP130: crystal structure, biophysical characterization, and interactions with antifungal azole drugs.
  J Biol Chem, 283, 5069-5080.
PDB codes: 2uuq 2uvn
18026129 J.D.Maréchal, C.A.Kemp, G.C.Roberts, M.J.Paine, C.R.Wolf, and M.J.Sutcliffe (2008).
Insights into drug metabolism by cytochromes P450 from modelling studies of CYP2D6-drug interactions.
  Br J Pharmacol, 153, S82-S89.  
18976212 K.N.Myasoedova (2008).
New findings in studies of cytochromes P450.
  Biochemistry (Mosc), 73, 965-969.  
18495666 N.Oezguen, S.Kumar, A.Hindupur, W.Braun, B.K.Muralidhara, and J.R.Halpert (2008).
Identification and analysis of conserved sequence motifs in cytochrome P450 family 2. Functional and structural role of a motif 187RFDYKD192 in CYP2B enzymes.
  J Biol Chem, 283, 21808-21816.  
18096676 P.Kang, M.Liao, M.R.Wester, J.S.Leeder, R.E.Pearce, and M.A.Correia (2008).
CYP3A4-Mediated carbamazepine (CBZ) metabolism: formation of a covalent CBZ-CYP3A4 adduct and alteration of the enzyme kinetic profile.
  Drug Metab Dispos, 36, 490-499.  
18611114 P.Urban, G.Truan, and D.Pompon (2008).
High-throughput enzymology and combinatorial mutagenesis for mining cytochrome P450 functions.
  Expert Opin Drug Metab Toxicol, 4, 733-747.  
17922078 Q.B.Su, F.He, X.D.Wang, S.Guan, Z.Y.Xie, L.Y.Wang, Y.J.Lu, L.Q.Gu, Z.S.Huang, X.Chen, M.Huang, and S.F.Zhou (2008).
Biotransformation and pharmacokinetics of the novel anticancer drug, SYUIQ-5, in the rat.
  Invest New Drugs, 26, 119-137.  
18619466 R.Fasan, Y.T.Meharenna, C.D.Snow, T.L.Poulos, and F.H.Arnold (2008).
Evolutionary history of a specialized p450 propane monooxygenase.
  J Mol Biol, 383, 1069-1080.
PDB code: 3cbd
  18924204 R.W.Gantt, R.D.Goff, G.J.Williams, and J.S.Thorson (2008).
Probing the aglycon promiscuity of an engineered glycosyltransferase.
  Angew Chem Int Ed Engl, 47, 8889-8892.  
18004755 W.Li, Y.Tang, H.Liu, J.Cheng, W.Zhu, and H.Jiang (2008).
Probing ligand binding modes of human cytochrome P450 2J2 by homology modeling, molecular dynamics simulation, and flexible molecular docking.
  Proteins, 71, 938-949.  
18431572 Z.Y.Zhang, B.M.King, R.D.Pelletier, and Y.N.Wong (2008).
Delineation of the interactions between the chemotherapeutic agent eribulin mesylate (E7389) and human CYP3A4.
  Cancer Chemother Pharmacol, 62, 707-716.  
17357170 A.Chougnet, Y.Grinkova, D.Ricard, S.Sligar, and W.D.Woggon (2007).
Fluorescent Probes for Rapid Screening of Potential Drug-Drug Interactions at the CYP3A4 Level.
  ChemMedChem, 2, 717-724.  
17459328 A.G.Roberts, and W.M.Atkins (2007).
Energetics of heterotropic cooperativity between alpha-naphthoflavone and testosterone binding to CYP3A4.
  Arch Biochem Biophys, 463, 89.  
17387527 A.R.Shaikh, E.Broclawik, H.Tsuboi, M.Koyama, A.Endou, H.Takaba, M.Kubo, C.A.Del Carpio, and A.Miyamoto (2007).
Oxidation mechanism in the metabolism of (S)-N-[1-(3-morpholin-4-ylphenyl)ethyl]-3-phenylacrylamide on oxyferryl active site in CYP3A4 Cytochrome: DFT modeling.
  J Mol Model, 13, 851-860.  
17534532 A.W.Munro, H.M.Girvan, and K.J.McLean (2007).
Variations on a (t)heme--novel mechanisms, redox partners and catalytic functions in the cytochrome P450 superfamily.
  Nat Prod Rep, 24, 585-609.  
17985934 A.Z.Kijac, Y.Li, S.G.Sligar, and C.M.Rienstra (2007).
Magic-angle spinning solid-state NMR spectroscopy of nanodisc-embedded human CYP3A4.
  Biochemistry, 46, 13696-13703.  
17311370 C.W.Locuson, P.M.Gannett, R.Ayscue, and T.S.Tracy (2007).
Use of simple docking methods to screen a virtual library for heteroactivators of cytochrome P450 2C9.
  J Med Chem, 50, 1158-1165.  
18020326 D.Fishelovitch, C.Hazan, H.Hirao, H.J.Wolfson, R.Nussinov, and S.Shaik (2007).
QM/MM study of the active species of the human cytochrome P450 3A4, and the influence thereof of the multiple substrate binding.
  J Phys Chem B, 111, 13822-13832.  
17933328 K.N.Myasoedova, A.M.Arutyunyan, and N.N.Magretova (2007).
Reconstitution of monooxygenase activity of membrane cytochromes P450 in vitro and detergents.
  Dokl Biochem Biophys, 415, 174-178.  
17705402 P.Lafite, F.André, D.C.Zeldin, P.M.Dansette, and D.Mansuy (2007).
Unusual regioselectivity and active site topology of human cytochrome P450 2J2.
  Biochemistry, 46, 10237-10247.  
17470359 P.Lafite, S.Dijols, D.C.Zeldin, P.M.Dansette, and D.Mansuy (2007).
Selective, competitive and mechanism-based inhibitors of human cytochrome P450 2J2.
  Arch Biochem Biophys, 464, 155-168.  
17549046 S.Ekins, J.Mestres, and B.Testa (2007).
In silico pharmacology for drug discovery: applications to targets and beyond.
  Br J Pharmacol, 152, 21-37.  
18005930 S.G.Rupasinghe, H.Duan, H.L.Frericks Schmidt, D.A.Berthold, C.M.Rienstra, and M.A.Schuler (2007).
High-yield expression and purification of isotopically labeled cytochrome P450 monooxygenases for solid-state NMR spectroscopy.
  Biochim Biophys Acta, 1768, 3061-3070.  
17887776 Y.Zhao, L.Sun, B.K.Muralidhara, S.Kumar, M.A.White, C.D.Stout, and J.R.Halpert (2007).
Structural and thermodynamic consequences of 1-(4-chlorophenyl)imidazole binding to cytochrome P450 2B4.
  Biochemistry, 46, 11559-11567.
PDB code: 2q6n
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.