1R9O - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF P4502C9 WITH FLURBIPROFEN BOUND

Authors :   M. R. Wester, J. K. Yano, G. A. Schoch, K. J. Griffin, C. D. Stout, E. F. Joh

Date :   30 Oct 03 (Deposition) - 15 Jun 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : A

Keywords :   P450, Monooxygenase, Drug Metabolizing Enzyme, Oxidoreductase, Heme (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. R. Wester, J. K. Yano, G. A. Schoch, C. Yang, K. J. Griffin, C. D. Stout E. F. Johnson
The Structure Of Human Cytochrome P450 2C9 Complexed With Flurbiprofen At 2. 0 A Resolution
J. Biol. Chem. V. 279 35630 2004
PubMed-ID: 15181000 | Reference-DOI: 10.1074/JBC.M405427200

Molecule 1 - CYTOCHROME P450 2C9
	Chains	:	A
	EC Number	:	1.14.14.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PCWORI
	Expression System Strain	:	DH5A
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	CATALYTIC DOMAIN
	Gene	:	CYP2C9
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	CYPIIC9, P450 PB-1, P450 MP-4, S-MEPHENYTOIN 4-HYDROXYLASE, P-450MP

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 3)

No.	Name	Count	Type	Full Name
1	FLP	1	Ligand/Ion	FLURBIPROFEN
2	GOL	1	Ligand/Ion	GLYCEROL
3	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:97 , ILE A:112 , VAL A:113 , TRP A:120 , ALA A:297 , GLY A:298 , THR A:301 , THR A:302 , THR A:305 , GLN A:356 , LEU A:362 , SER A:365 , HIS A:368 , PRO A:427 , PHE A:428 , SER A:429 , ARG A:433 , CYS A:435 , VAL A:436 , GLY A:437 , ALA A:441 , GLU A:444 , HOH A:600 , HOH A:696	BINDING SITE FOR RESIDUE HEM A 500
2	AC2	SOFTWARE	ARG A:108 , ASN A:204 , ILE A:205 , LEU A:208 , MET A:240 , ASP A:293 , GLY A:296 , ALA A:297 , HOH A:600	BINDING SITE FOR RESIDUE FLP A 501
3	AC3	SOFTWARE	ILE A:205 , GLU A:300 , ALA A:477	BINDING SITE FOR RESIDUE GOL A 502

(no "SS Bond" information available for 1R9O)

Asymmetric/Biological Unit

No.	Residues
1	Gln A:278	-	Pro A:279

Asymmetric/Biological Unit (16, 16)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_075286	R	125	H	CP2C9_HUMAN	Polymorphism	72558189	A	R	125	H
02	UniProt	VAR_075287	R	125	L	CP2C9_HUMAN	Polymorphism	---	A	R	125	L
03	UniProt	VAR_008343	R	144	C	CP2C9_HUMAN	Polymorphism	1799853	A	R	144	C
04	UniProt	VAR_018863	R	150	H	CP2C9_HUMAN	Polymorphism	7900194	A	R	150	H
05	UniProt	VAR_075288	N	204	H	CP2C9_HUMAN	Polymorphism	---	A	N	204	H
06	UniProt	VAR_018864	H	251	R	CP2C9_HUMAN	Polymorphism	2256871	A	H	251	R
07	UniProt	VAR_018865	E	272	G	CP2C9_HUMAN	Polymorphism	9332130	A	E	272	G
08	UniProt	VAR_018866	R	335	W	CP2C9_HUMAN	Polymorphism	28371685	A	R	335	W
09	UniProt	VAR_008344	Y	358	C	CP2C9_HUMAN	Polymorphism	1057909	A	Y	358	C
10	UniProt	VAR_008345	I	359	L	CP2C9_HUMAN	Polymorphism	1057910	A	I	359	L
11	UniProt	VAR_013515	I	359	T	CP2C9_HUMAN	Polymorphism	56165452	A	I	359	T
12	UniProt	VAR_013516	D	360	E	CP2C9_HUMAN	Polymorphism	28371686	A	D	360	E
13	UniProt	VAR_024717	L	413	P	CP2C9_HUMAN	Polymorphism	28371687	A	L	413	P
14	UniProt	VAR_008346	G	417	D	CP2C9_HUMAN	Polymorphism	---	A	G	417	D
15	UniProt	VAR_075289	I	434	F	CP2C9_HUMAN	Polymorphism	---	A	I	434	F
16	UniProt	VAR_018867	P	489	S	CP2C9_HUMAN	Polymorphism	9332239	A	P	489	S

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CYTOCHROME_P450	PS00086	Cytochrome P450 cysteine heme-iron ligand signature.	CP2C9_HUMAN	428-437	1	A:428-437

Asymmetric/Biological Unit (9, 9)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1b	ENST00000260682	1b	ENSE00001809652	chr10:96698428-96698607	180	CP2C9_HUMAN	1-56	56	1	A:26-56 (gaps)	31
1.2a	ENST00000260682	2a	ENSE00001662713	chr10:96701615-96701777	163	CP2C9_HUMAN	57-111	55	1	A:57-111	55
1.3a	ENST00000260682	3a	ENSE00001730103	chr10:96701949-96702098	150	CP2C9_HUMAN	111-161	51	1	A:111-161	51
1.4	ENST00000260682	4	ENSE00001595620	chr10:96707536-96707696	161	CP2C9_HUMAN	161-214	54	1	A:161-213	53
1.5a	ENST00000260682	5a	ENSE00001711217	chr10:96708865-96709041	177	CP2C9_HUMAN	215-273	59	1	A:221-273	53
1.6	ENST00000260682	6	ENSE00001653852	chr10:96731861-96732002	142	CP2C9_HUMAN	274-321	48	1	A:274-321	48
1.7	ENST00000260682	7	ENSE00001785730	chr10:96740940-96741127	188	CP2C9_HUMAN	321-383	63	1	A:321-383	63
1.8	ENST00000260682	8	ENSE00001603154	chr10:96745790-96745931	142	CP2C9_HUMAN	384-431	48	1	A:384-431	48
1.9	ENST00000260682	9	ENSE00001162173	chr10:96748604-96749147	544	CP2C9_HUMAN	431-490	60	1	A:431-490	60

Asymmetric/Biological 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:455
 aligned with CP2C9_HUMAN | P11712 from UniProtKB/Swiss-Prot  Length:490

    Alignment length:467
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          490  
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485    |  
          CP2C9_HUMAN    26 RGKLPPGPTPLPVIGNILQIGIKDISKSLTNLSKVYGPVFTLYFGLKPIVVLHGYEAVKEALIDLGEEFSGRGIFPLAERANRGFGIVFSNGKKWKEIRRFSLMTLRNFGMGKRSIEDRVQEEARCLVEELRKTKASPCDPTFILGCAPCNVICSIIFHKRFDYKDQQFLNLMEKLNENIKILSSPWIQICNNFSPIIDYFPGTHNKLLKNVAFMKSYILEKVKEHQESMDMNNPQDFIDCFLMKMEKEKHNQPSEFTIESLENTAVDLFGAGTETTSTTLRYALLLLLKHPEVTAKVQEEIERVIGRNRSPCMQDRSHMPYTDAVVHEVQRYIDLLPTSLPHAVTCDIKFRNYLIPKGTTILISLTSVLHDNKEFPNPEMFDPHHFLDEGGNFKKSKYFMPFSAGKRICVGEALAGMELFLFLTSILQNFNLKSLVDPKNLDTTPVVNGFASVPPFYQLCFIPV--   -
               SCOP domains d1r9oa_ A: M     ammalian cytochrome p450 2c9                                                                                                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 1r9oA00 A:26     -492 Cytochrome p450                                                                                                                                                                                                                                                                                                                                                                                                                                               CATH domains
               Pfam domains ----p450-1r9     oA01 A:30-487                                                                                                                                                                                                                                                                                                                                                                                                                                                ----- Pfam domains
         Sec.struct. author ............-----...hhhhhhhhhhhhhhhhh.eeeee....eeeee.hhhhhhhhhh.......ee..................hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh....-------........hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh.......ee....eee..eee....eeee.hhhhhh...........hhhhhh................hhhhh..hhhhhhhhhhhhhhhhhhheeeee..hhhhh.................eeeee... Sec.struct. author
             SAPs(SNPs) (1) ---------------------------------------------------------------------------------------------------H------------------C-----H-----------------------------------------------------H----------------------------------------------R--------------------G--------------------------------------------------------------W----------------------CLE----------------------------------------------------P---D----------------F------------------------------------------------------S--- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ---------------------------------------------------------------------------------------------------L-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYTOCHROME------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1b  PDB: A:26-56 (gaps) Exon 1.2a  PDB: A:57-111 UniProt: 57-111               -------------------------------------------------Exon 1.4  PDB: A:161-213 UniProt: 161-214 [INCOMPLETE]Exon 1.5a  PDB: A:221-273 UniProt: 215-273 [INCOMPLETE]    Exon 1.6  PDB: A:274-321 UniProt: 274-321       --------------------------------------------------------------Exon 1.8  PDB: A:384-431 UniProt: 384-431       ------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------Exon 1.3a  PDB: A:111-161 UniProt: 111-161         ---------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.7  PDB: A:321-383 UniProt: 321-383                      -----------------------------------------------Exon 1.9  PDB: A:431-490 UniProt: 431-490                   -- Transcript 1 (2)
                 1r9o A  26 RGKLPPGPTPLP-----LQIGIKDISKSLTNLSKVYGPVFTLYFGLKPIVVLHGYEAVKEALIDLGEEFSGRGIFPLAERANRGFGIVFSNGKKWKEIRRFSLMTLRNFGMGKRSIEDRVQEEARCLVEELRKTKASPCDPTFILGCAPCNVICSIIFHKRFDYKDQQFLNLMEKLNENIKILSSPWI-------PIIDYFPGTHNKLLKNVAFMKSYILEKVKEHQESMDMNNPQDFIDCFLMKMEKEKHNQPSEFTIESLENTAVDLFGAGTETTSTTLRYALLLLLKHPEVTAKVQEEIERVIGRNRSPCMQDRSHMPYTDAVVHEVQRYIDLLPTSLPHAVTCDIKFRNYLIPKGTTILISLTSVLHDNKEFPNPEMFDPHHFLDEGGNFKKSKYFMPFSAGKRICVGEALAGMELFLFLTSILQNFNLKSLVDPKNLDTTPVVNGFASVPPFYQLCFIPIHH 492
                                    35 |     |45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       | -     | 225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       
                                      37    43                                                                                                                                                                       213     221

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Cytochrome P450 (480)

Superfamily: Cytochrome P450 (480)

Family: Cytochrome P450 (323)

Protein domain: Mammalian cytochrome p450 2c9 (3)

Human (Homo sapiens) [TaxId: 9606] (3)

d1r9oa_

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Cytochrome p450 (271)

Homologous Superfamily: Cytochrome p450 (271)

Human (Homo sapiens) (32)

1r9oA00

A:26-492

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: p450] (161)

Family: p450 (161)

Homo sapiens (Human) (33)

p450-1r9oA01

A:30-487

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (CP2C9_HUMAN | P11712)

molecular function
	GO:0052741	(R)-limonene 6-monooxygenase activity	Catalysis of the reaction: (4R)-limonene + H+ + NADPH + O2 = (1R,5S)-carveol + H2O + NADP+.
	GO:0018675	(S)-limonene 6-monooxygenase activity	Catalysis of the reaction: (-)-limonene + NADPH + H+ + O2 = (-)-trans-carveol + NADP+ + H2O.
	GO:0018676	(S)-limonene 7-monooxygenase activity	Catalysis of the reaction: (4S)-limonene + H(+) + NADPH + O(2) = (4S)-perillyl alcohol + H(2)O + NADP(+).
	GO:0008392	arachidonic acid epoxygenase activity	Catalysis of an NADPH- and oxygen-dependent reaction that converts arachidonic acid to a cis-epoxyeicosatrienoic acid.
	GO:0034875	caffeine oxidase activity	Catalysis of the reaction: caffeine + O2 + 2 H+ + 2 e- = 1,3,7-trimethyluric acid + H2O.
	GO:0001567	cholesterol 25-hydroxylase activity	Catalysis of the reaction: AH(2) + cholesterol + O(2) = 25-hydroxycholesterol + A + H(2)O.
	GO:0008144	drug binding	Interacting selectively and non-covalently with a drug, any naturally occurring or synthetic substance, other than a nutrient, that, when administered or applied to an organism, affects the structure or functioning of the organism; in particular, any such substance used in the diagnosis, prevention, or treatment of disease.
	GO:0020037	heme binding	Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
	GO:0005506	iron ion binding	Interacting selectively and non-covalently with iron (Fe) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004497	monooxygenase activity	Catalysis of the incorporation of one atom from molecular oxygen into a compound and the reduction of the other atom of oxygen to water.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0016705	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen	Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from each of two donors, and molecular oxygen is reduced or incorporated into a donor.
	GO:0019825	oxygen binding	Interacting selectively and non-covalently with oxygen (O2).
	GO:0008395	steroid hydroxylase activity	Catalysis of the formation of a hydroxyl group on a steroid by incorporation of oxygen from O2.
biological process
	GO:0043603	cellular amide metabolic process	The chemical reactions and pathways involving an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group, as carried out by individual cells.
	GO:0042737	drug catabolic process	The chemical reactions and pathways resulting in the breakdown of a drug, a substance used in the diagnosis, treatment or prevention of a disease.
	GO:0017144	drug metabolic process	The chemical reactions and pathways involving a drug, a substance used in the diagnosis, treatment or prevention of a disease; as used here antibiotic substances (see antibiotic metabolism) are considered to be drugs, even if not used in medical or veterinary practice.
	GO:0019373	epoxygenase P450 pathway	The chemical reactions and pathways by which arachidonic acid is converted to other compounds including epoxyeicosatrienoic acids and dihydroxyeicosatrienoic acids.
	GO:0042738	exogenous drug catabolic process	The chemical reactions and pathways resulting in the breakdown of a drug that has originated externally to the cell or organism.
	GO:0006629	lipid metabolic process	The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
	GO:0032787	monocarboxylic acid metabolic process	The chemical reactions and pathways involving monocarboxylic acids, any organic acid containing one carboxyl (COOH) group or anion (COO-).
	GO:0016098	monoterpenoid metabolic process	The chemical reactions and pathways involving monoterpenoid compounds, terpenoids having a C10 skeleton.
	GO:0097267	omega-hydroxylase P450 pathway	The chemical reactions and pathways by which arachidonic acid is converted to other compounds initially by omega-hydroxylation.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0070989	oxidative demethylation	The process of removing one or more methyl groups from a molecule, involving the oxidation (i.e. electron loss) of one or more atoms in the substrate.
	GO:0008202	steroid metabolic process	The chemical reactions and pathways involving steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus.
	GO:0019627	urea metabolic process	The chemical reactions and pathways involving urea, the water soluble compound O=C-(NH2)2.
	GO:0006805	xenobiotic metabolic process	The chemical reactions and pathways involving a xenobiotic compound, a compound foreign to living organisms. Used of chemical compounds, e.g. a xenobiotic chemical, such as a pesticide.
cellular component
	GO:0005783	endoplasmic reticulum	The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
	GO:0005789	endoplasmic reticulum membrane	The lipid bilayer surrounding the endoplasmic reticulum.
	GO:0043231	intracellular membrane-bounded organelle	Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0031090	organelle membrane	A membrane that is one of the two lipid bilayers of an organelle envelope or the outermost membrane of single membrane bound organelle.

Asymmetric/Biological Unit
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		Gln A:278 - Pro A:279	[ RasMol ]

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	1r9o
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	1.14.14.1
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UniProtKB/Swiss-Prot
	CP2C9_HUMAN \| P11712	:	1og2 1og5 4nz2 5a5i 5a5j 5k7k

1n6b	MICROSOMAL CYTOCHROME P450 2C5/3LVDH COMPLEX WITH A DIMETHYL DERIVATIVE OF SULFAPHENAZOLE
1nr6	MICROSOMAL CYTOCHROME P450 2C5/3LVDH COMPLEX WITH DICLOFENAC
1og5	STRUCTURE OF HUMAN CYTOCHROME P450 CYP2C9
1po5	STRUCTURE OF MAMMALIAN CYTOCHROME P450 2B4
1pq2	CRYSTAL STRUCTURE OF HUMAN DRUG METABOLIZING CYTOCHROME P450 2C8

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (16, 16)

PROSITE Motifs (1, 1)

Exons (9, 9)

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SCOP Domains (1, 1)

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Pfam Domains (1, 1)

Gene Ontology (34, 34)

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