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(-) Description

Title :  CRYSTAL STRUCTURE OF CYP2C9 IN COMPLEX WITH AN INHIBITOR
 
Authors :  G. Branden, T. Sjogren, Y. Xue
Date :  11 Dec 13  (Deposition) - 13 Aug 14  (Release) - 13 Aug 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.45
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Cytochrome P-450, Cyp2C9, Inhibitor, Structure-Based Drug Design, Drug Metabolism, Monooxygenase, Oxidoreductase-Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Branden, T. Sjogren, V. Schnecke, Y. Xue
Structure-Based Ligand Design To Overcome Cyp Inhibition In Drug Discovery Projects.
Drug Discov Today V. 19 905 2014
PubMed-ID: 24642031  |  Reference-DOI: 10.1016/J.DRUDIS.2014.03.012

(-) Compounds

Molecule 1 - CYTOCHROME P450 2C9
    Chains: A, B
    EC Number: 1.14.13.-, 1.14.13.80, 1.14.13.48, 1.14.13.49
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: XL1 BLUE
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 30-490
    Gene: CYP2C10, CYP2C9, CYP2C9 CYP2C10
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: (R)-LIMONENE 6-MONOOXYGENASE, (S)-LIMONENE 6-MONOOXYGENASE, (S)-LIMONENE 7-MONOOXYGENASE, CYPIIC9, CYTOCHROME P-450MP, CYTOCHROME P450 MP-4, CYTOCHROME P450 MP-8, CYTOCHROME P450 PB-1, S-MEPHENYTOIN 4-HYDROXYLASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric Unit (4, 8)
No.NameCountTypeFull Name
12QJ2Ligand/Ion(2R)-N-{4-[(3-BROMOPHENYL)SULFONYL]-2-CHLOROPHENYL}-3,3,3-TRIFLUORO-2-HYDROXY-2-METHYLPROPANAMIDE
2GOL2Ligand/IonGLYCEROL
3HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
4SO42Ligand/IonSULFATE ION
Biological Unit 1 (4, 4)
No.NameCountTypeFull Name
12QJ1Ligand/Ion(2R)-N-{4-[(3-BROMOPHENYL)SULFONYL]-2-CHLOROPHENYL}-3,3,3-TRIFLUORO-2-HYDROXY-2-METHYLPROPANAMIDE
2GOL1Ligand/IonGLYCEROL
3HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
4SO41Ligand/IonSULFATE ION
Biological Unit 2 (4, 4)
No.NameCountTypeFull Name
12QJ1Ligand/Ion(2R)-N-{4-[(3-BROMOPHENYL)SULFONYL]-2-CHLOROPHENYL}-3,3,3-TRIFLUORO-2-HYDROXY-2-METHYLPROPANAMIDE
2GOL1Ligand/IonGLYCEROL
3HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
4SO41Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:97 , ILE A:112 , VAL A:113 , TRP A:120 , ARG A:124 , LEU A:294 , ALA A:297 , GLY A:298 , THR A:301 , THR A:302 , GLN A:356 , LEU A:361 , LEU A:362 , SER A:365 , HIS A:368 , PRO A:427 , PHE A:428 , SER A:429 , ARG A:433 , CYS A:435 , GLY A:437 , ALA A:441 , HOH A:647BINDING SITE FOR RESIDUE HEM A 501
2AC2SOFTWAREPHE A:100 , THR A:364 , SER A:365 , PRO A:367 , PHE A:476 , SO4 A:503 , HOH A:631BINDING SITE FOR RESIDUE GOL A 502
3AC3SOFTWARELEU A:208 , GOL A:502 , 2QJ A:504BINDING SITE FOR RESIDUE SO4 A 503
4AC4SOFTWAREALA A:106 , ASN A:107 , PHE A:114 , LEU A:233 , GLY A:296 , THR A:301 , THR A:304 , LEU A:362 , LEU A:366 , ALA A:477 , SO4 A:503 , HOH A:681 , HOH A:695BINDING SITE FOR RESIDUE 2QJ A 504
5AC5SOFTWAREARG B:97 , ILE B:112 , VAL B:113 , TRP B:120 , ARG B:124 , LEU B:294 , ALA B:297 , GLY B:298 , THR B:301 , THR B:302 , THR B:305 , GLN B:356 , LEU B:362 , SER B:365 , HIS B:368 , PRO B:427 , PHE B:428 , SER B:429 , ARG B:433 , CYS B:435 , GLY B:437 , ALA B:441 , HOH B:755BINDING SITE FOR RESIDUE HEM B 501
6AC6SOFTWAREPHE B:100 , THR B:364 , SER B:365 , PRO B:367 , PHE B:476 , SO4 B:503BINDING SITE FOR RESIDUE GOL B 502
7AC7SOFTWARELEU B:208 , GOL B:502 , 2QJ B:504 , HOH B:668BINDING SITE FOR RESIDUE SO4 B 503
8AC8SOFTWAREASN B:107 , PHE B:114 , ILE B:205 , VAL B:237 , GLY B:296 , GLU B:300 , THR B:301 , THR B:304 , LEU B:362 , ALA B:477 , SO4 B:503 , HOH B:682 , HOH B:758BINDING SITE FOR RESIDUE 2QJ B 504

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4NZ2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4NZ2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4NZ2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4NZ2)

(-) Exons   (0, 0)

(no "Exon" information available for 4NZ2)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:464
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhhh..hhhhhhhhhhhhhh.eeeeee..eeeeee.hhhhhhhhhh.......ee..hhhhhhhh........hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh.......ee....eee..eee....eeee.hhhhhh...........hhhhhh................hhhhh..hhhhhhhhhhhhhhhhhhheeeee...........ee....ee.....eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nz2 A  27 KGRPPGPTPLPVIGNILQIGIKDISKSLTNLSKVYGPVFTLYFGLKPIVVLHGYEAVKEALIDLGEEFSGRGIFPLAERANRGFGIVFSNGKKWKEIRRFSLMTLRNFGMGKRSIEDRVQEEARCLVEELRKTKASPCDPTFILGCAPCNVICSIIFHKRFDYKDQQFLNLMEKLNENIEILSSPWIQVYNNFPALLDYFPGTHNKLLKNVAFMKSYILEKVKEHQESMDMNNPQDFIDCFLMKMEKEKHNQPSEFTIESLENTAVDLFGAGTETTSTTLRYALLLLLKHPEVTAKVQEEIERVIGRNRSPCMQDRSHMPYTDAVVHEVQRYIDLLPTSLPHAVTCDIKFRNYLIPKGTTILISLTSVLHDNKEFPNPEMFDPHHFLDEGGNFKKSKYFMPFSAGKRICVGEALAGMELFLFLTSILQNFNLKSLVDPKNLDTTPVVNGFASVPPFYQLCFIPV 490
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486    


Chain B from PDB  Type:PROTEIN  Length:464
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhhh..hhhhhhhhhhhhhh.eeeeee..eeeeee.hhhhhhhhhh.......ee..hhhhhhhh.........hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh.......ee....eee..eee....eeeehhhhhhh...........hhhhhh.......................hhhhhhhhhhhhhhhhhhheeeee...........ee....ee.....eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nz2 B  27 KGRPPGPTPLPVIGNILQIGIKDISKSLTNLSKVYGPVFTLYFGLKPIVVLHGYEAVKEALIDLGEEFSGRGIFPLAERANRGFGIVFSNGKKWKEIRRFSLMTLRNFGMGKRSIEDRVQEEARCLVEELRKTKASPCDPTFILGCAPCNVICSIIFHKRFDYKDQQFLNLMEKLNENIEILSSPWIQVYNNFPALLDYFPGTHNKLLKNVAFMKSYILEKVKEHQESMDMNNPQDFIDCFLMKMEKEKHNQPSEFTIESLENTAVDLFGAGTETTSTTLRYALLLLLKHPEVTAKVQEEIERVIGRNRSPCMQDRSHMPYTDAVVHEVQRYIDLLPTSLPHAVTCDIKFRNYLIPKGTTILISLTSVLHDNKEFPNPEMFDPHHFLDEGGNFKKSKYFMPFSAGKRICVGEALAGMELFLFLTSILQNFNLKSLVDPKNLDTTPVVNGFASVPPFYQLCFIPV 490
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4NZ2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4NZ2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4NZ2)

(-) Gene Ontology  (34, 34)

Asymmetric Unit(hide GO term definitions)

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(-) Related Entries Specified in the PDB File

4ny4