Structure of PDB 3gph Chain A Binding Site BS02

Receptor Information

>3gph Chain A (length=461) Species: 9606 (Homo sapiens)

KLPPGPFPLPIIGNLFQLELKNIPKSFTRLAQRFGPVFTLYVGSQRMVVM
HGYKAVKEALLDYKDEFSGRGDLPAFHAHRDRGIIFNNGPTWKDIRRFSL
TTLRNYGKQGNESRIQREAHFLLEALRKTQGQPFDPTFLIGCAPCNVIAD
ILFRKHFDYNDEKFLRLMYLFNENFHLLSTPWLQLYNNFPSFLHYLPGSH
RKVIKNVAEVKEYVSERVKEHHQSLDPNCPRDLTDCLLVEMEKEKHSAER
LYTMDGITVTVADLFFAGTETTSTTLRYGLLILMKYPEIEEKLHEEIDRV
IGPSRIPAIKDRQEMPYMDAVVHEIQRFITLVPSNLPHEATRDTIFRGYL
IPKGTVVVPTLDSVLYDNQEFPDPEKFKPEHFLNENGKFKYSDYFKPFST
GKRVCAGEGLARMELFLLLCAILQHFNLKPLVDPKDIDLSPIHIGFGCIP
PRYKLCVIPRS

Ligand information

• Ligand ID: OID
• InChI: InChI=1S/C13H22N2O2/c16-13(17)8-6-4-2-1-3-5-7-10-15-11-9-14-12-15/h9,11-12H,1-8,10H2,(H,16,17)
• InChIKey: DOJPUPKORVKCJK-UHFFFAOYSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1cn(cn1)CCCCCCCCCC(=O)O
  CACTVS 3.341: OC(=O)CCCCCCCCCn1ccnc1
  ACDLabs 10.04: O=C(O)CCCCCCCCCn1ccnc1
• Formula: C13 H22 N2 O2
• Name: 10-(1H-imidazol-1-yl)decanoic acid;
  10-imidazolyl-decanoic acid
• ZINC: ZINC000039296093
• PDB chain: 3gph Chain A Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3gph Human cytochrome P450 2E1 structures with fatty acid analogs reveal a previously unobserved binding mode.
• Resolution: 2.7 Å
• Binding residue (original residue number in PDB): F203 N206 F207 V242 F298 T303
• Binding residue (residue number reindexed from 1): F171 N174 F175 V210 F266 T271
• Annotation score: 2
• Binding affinity: BindingDB: Kd=9.0e+3nM

Enzymatic activity

• Catalytic site (original residue number in PDB): T303 F430 C437
• Catalytic site (residue number reindexed from 1): T271 F398 C405
• Enzyme Commision number: 1.14.13.n7: 4-nitrophenol 2-hydroxylase.
  1.14.14.1: unspecific monooxygenase.

Gene Ontology

Molecular Function

• GO:0004497 monooxygenase activity
• GO:0005506 iron ion binding
• GO:0008392 arachidonate epoxygenase activity
• GO:0016491 oxidoreductase activity
• GO:0016705 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
• GO:0016709 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen
• GO:0016712 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen
• GO:0018601 4-nitrophenol 2-monooxygenase activity
• GO:0019825 oxygen binding
• GO:0019899 enzyme binding
• GO:0020037 heme binding
• GO:0030544 Hsp70 protein binding
• GO:0046872 metal ion binding
• GO:0051879 Hsp90 protein binding
• GO:0070330 aromatase activity
• GO:0120319 long-chain fatty acid omega-1 hydroxylase activity

Biological Process

• GO:0001676 long-chain fatty acid metabolic process
• GO:0002933 lipid hydroxylation
• GO:0006631 fatty acid metabolic process
• GO:0006805 xenobiotic metabolic process
• GO:0008202 steroid metabolic process
• GO:0009617 response to bacterium
• GO:0016098 monoterpenoid metabolic process
• GO:0018885 carbon tetrachloride metabolic process
• GO:0018910 benzene metabolic process
• GO:0018960 4-nitrophenol metabolic process
• GO:0019373 epoxygenase P450 pathway
• GO:0042197 halogenated hydrocarbon metabolic process
• GO:0042759 long-chain fatty acid biosynthetic process

Cellular Component

• GO:0005737 cytoplasm
• GO:0005739 mitochondrion
• GO:0005743 mitochondrial inner membrane
• GO:0005783 endoplasmic reticulum
• GO:0005789 endoplasmic reticulum membrane
• GO:0043231 intracellular membrane-bounded organelle

External links

• PDB: RCSB:3gph, PDBe:3gph, PDBj:3gph
• PDBsum: 3gph
• PubMed: 20463018
• UniProt: P05181|CP2E1_HUMAN Cytochrome P450 2E1 (Gene Name=CYP2E1)