Structure of PDB 3pm5 Chain D Binding Site BS04

Receptor Information
>3pm5 Chain D (length=469) Species: 59406 (Aromatoleum evansii) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SERIPNNVNLNENKTLQRALEQWQPSFLNWWDDMGPENSSNYDVYLRTAV
SVDPKGWADFGYVKMHDYRWGIFLAPQEGEKKITFGEHKGQDVWQEVPGE
YRSTLRRIIVTQGDTEPASVEQQRHLGLTAPSLYDLRNLFQVNVEEGRHL
WAMVYLLHAHFGRDGREEGEALLERRSGDEDNPRILTAFNEKTPDWLSFF
MFTFITDRDGKFQLASLAESAFDPLARTCKFMLTEEAHHLFVGESGIARV
IQRTCEVMKELGTDDPAKLRAAGVIDLPTLQKYLNFHYSVTSDLYGAEIS
SNAATYYTNGLKGRFEEEKIGDDHKLQNSEYEVMDVAGDKILTRHVPALS
ALNERLRDDWITDVQAGVDRWNRIPAKFGFDFRFTLPHKGFHRKIGMFAD
VHVSPDGRLISEAEWTHQHKNWLPTESDRLYVHSLMGRCLEPGKFANWIA
APARGINNQPVNFEYVRFN
Ligand information
Ligand IDBYC
InChIInChI=1S/C28H40N7O17P3S/c1-28(2,22(38)25(39)31-9-8-18(36)30-10-11-56-27(40)16-6-4-3-5-7-16)13-49-55(46,47)52-54(44,45)48-12-17-21(51-53(41,42)43)20(37)26(50-17)35-15-34-19-23(29)32-14-33-24(19)35/h3-7,14-15,17,20-22,26,37-38H,8-13H2,1-2H3,(H,30,36)(H,31,39)(H,44,45)(H,46,47)(H2,29,32,33)(H2,41,42,43)/t17-,20-,21-,22+,26-/m1/s1
InChIKeyVEVJTUNLALKRNO-TYHXJLICSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0CC(C)(COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)C(C(=O)NCCC(=O)NCCSC(=O)c4ccccc4)O
ACDLabs 12.01O=C(SCCNC(=O)CCNC(=O)C(O)C(C)(C)COP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3OP(=O)(O)O)c4ccccc4
OpenEye OEToolkits 1.7.0CC(C)(CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)[C@H](C(=O)NCCC(=O)NCCSC(=O)c4ccccc4)O
CACTVS 3.370CC(C)(CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[CH](O)C(=O)NCCC(=O)NCCSC(=O)c4ccccc4
CACTVS 3.370CC(C)(CO[P](O)(=O)O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[C@@H](O)C(=O)NCCC(=O)NCCSC(=O)c4ccccc4
FormulaC28 H40 N7 O17 P3 S
Namebenzoyl coenzyme A
ChEMBL
DrugBank
ZINCZINC000008551184
PDB chain3pm5 Chain D Residue 1003 [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]
PDB3pm5 Structure and Mechanism of the Diiron Benzoyl-Coenzyme A Epoxidase BoxB.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		Q116 T119 E120 S123 F193 D211 D213 G214 S304 N306 K316 I399
Binding residue
(residue number reindexed from 1)		Q112 T115 E116 S119 F189 D207 D209 G210 S300 N302 K312 I395
Annotation score4
Enzymatic activity
Enzyme Commision number 1.14.13.208: benzoyl-CoA 2,3-epoxidase.
Gene Ontology
Molecular Function
GO:0016491 oxidoreductase activity
GO:0046872 metal ion binding
GO:0051213 dioxygenase activity
Biological Process
GO:0009056 catabolic process
GO:0010124 phenylacetate catabolic process
Cellular Component
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3pm5, PDBe:3pm5, PDBj:3pm5
PDBsum3pm5
PubMed21632537
UniProtQ9AIX7|BOXB_AROEV Benzoyl-CoA oxygenase component B (Gene Name=boxB)

[Back to BioLiP]