Structure of PDB 2hmk Chain A Binding Site BS03

Receptor Information
>2hmk Chain A (length=446) Species: 306 (Pseudomonas sp.) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MNYNNKILVSESGLSQKHLIHGDEELFQHELKTIFARNWLFLTHDSLIPA
PGDYVTAKMGIDEVIVSRQNDGSIRAFLNVCRHRGKTLVSVEAGNAKGFV
CSYHGWGFGSNGELQSVPFEKDLYGESLNKKCLGLKEVARVESFHGFIYG
CFDQEAPPLMDYLGDAAWYLEPMFKHSGGLELVGPPGKVVIKANWKAPAE
NFVGDAYHVGWTHASSLRSGESIFSSLAGNAALPPEGAGLQMTSKYGSGM
GVLWDGYSGVHSADLVPELMAFGGAKQERLNKEIGDVRARIYRSHLNCTV
FPNNSMLTCSGVFKVWNPIDANTTEVWTYAIVEKDMPEDLKRRLADSVQR
TFGPAGFWESDDNDNMETASQNGKKYQSRDSDLLSNLGFGEDVYGDAVYP
GVVGKSAIGETSYRGFYRAYQAHVSSSNWAEFEHASSTWHTELTKT
Ligand information
Ligand IDPEY
InChIInChI=1S/C14H10/c1-3-7-13-11(5-1)9-10-12-6-2-4-8-14(12)13/h1-10H
InChIKeyYNPNZTXNASCQKK-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341c1ccc2c(c1)ccc3ccccc23
ACDLabs 10.04c3cc2ccc1ccccc1c2cc3
OpenEye OEToolkits 1.5.0c1ccc2c(c1)ccc3c2cccc3
FormulaC14 H10
NamePHENANTHRENE
ChEMBLCHEMBL46730
DrugBank
ZINCZINC000000967819
PDB chain2hmk Chain A Residue 701 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB2hmk Structural basis for regioselectivity and stereoselectivity of product formation by naphthalene 1,2-dioxygenase.
Resolution1.65 Å
Binding residue
(original residue number in PDB)		N201 D205 H208 V209 F224 N297
Binding residue
(residue number reindexed from 1)		N201 D205 H208 V209 F224 N297
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) H104 D205 H208 H213 D362
Catalytic site (residue number reindexed from 1) H104 D205 H208 H213 D362
Enzyme Commision number 1.14.12.12: naphthalene 1,2-dioxygenase.
Gene Ontology
Molecular Function
GO:0005506 iron ion binding
GO:0018625 naphthalene 1,2-dioxygenase activity
GO:0046872 metal ion binding
GO:0051213 dioxygenase activity
GO:0051537 2 iron, 2 sulfur cluster binding
Biological Process
GO:0009056 catabolic process
GO:0044237 cellular metabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2hmk, PDBe:2hmk, PDBj:2hmk
PDBsum2hmk
PubMed16980501
UniProtP0A111|NDOB_PSEU8 Naphthalene 1,2-dioxygenase system, large oxygenase component (Gene Name=doxB)

[Back to BioLiP]