Structure of PDB 2yoo Chain D Binding Site BS02

Receptor Information
>2yoo Chain D (length=394) Species: 246196 (Mycolicibacterium smegmatis MC2 155) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TRPDVDLVNGMFYADGGAREAYRWMRANEPVFRDRNGLAAATTYQAVLDA
ERNPELFSSTGGIRPDQPGMPYMIDMDDPQHLLRRKLVNAGFTRKRVMDK
VDSIGRLCDTLIDAVCERGECDFVRDIAAPLPMAVIGDMLGVLPTERDML
LKWSDDLVCGLSSHVDEAAIQKLMDTFAAYTEFTKDVITKRRAEPTDDLF
SVLVNSEVEGQRMSDDEIVFETLLILIGGDETTRHTLSGGTEQLLRHRDQ
WDALVADVDLLPGAIEEMLRWTSPVKNMCRTLTADTVFHGTELRAGEKIM
LMFESANFDESVFGDPDNFRIDRNPNSHVAFGFGTHFCLGNQLARLELRL
MTERVLRRLPDLRLADDAPVPLRPANFVSGPESMPVVFTPSAPV
Ligand information
Ligand IDK2B
InChIInChI=1S/C27H44O/c1-18(2)7-6-8-19(3)23-11-12-24-22-10-9-20-17-21(28)13-15-26(20,4)25(22)14-16-27(23,24)5/h17-19,22-25H,6-16H2,1-5H3/t19-,22+,23-,24+,25+,26+,27-/m1/s1
InChIKeyNYOXRYYXRWJDKP-GYKMGIIDSA-N
SMILES
SoftwareSMILES
CACTVS 3.352CC(C)CCC[CH](C)[CH]1CC[CH]2[CH]3CCC4=CC(=O)CC[C]4(C)[CH]3CC[C]12C
OpenEye OEToolkits 1.6.1CC(C)CCC[C@@H](C)[C@H]1CC[C@@H]2[C@@]1(CC[C@H]3[C@H]2CCC4=CC(=O)CC[C@]34C)C
OpenEye OEToolkits 1.6.1CC(C)CCCC(C)C1CCC2C1(CCC3C2CCC4=CC(=O)CCC34C)C
CACTVS 3.352CC(C)CCC[C@@H](C)[C@H]1CC[C@H]2[C@@H]3CCC4=CC(=O)CC[C@]4(C)[C@H]3CC[C@]12C
ACDLabs 10.04O=C4C=C2C(C1CCC3(C(C1CC2)CCC3C(C)CCCC(C)C)C)(C)CC4
FormulaC27 H44 O
Name(8ALPHA,9BETA)-CHOLEST-4-EN-3-ONE
ChEMBLCHEMBL63243
DrugBank
ZINCZINC000100060554
PDB chain2yoo Chain D Residue 1404 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2yoo A Highly Conserved Mycobacterial Cholesterol Catabolic Pathway.
Resolution1.69 Å
Binding residue
(original residue number in PDB)		M179 F182 L229 I232 F382
Binding residue
(residue number reindexed from 1)		M174 F177 L224 I227 F377
Annotation score5
Binding affinityMOAD: Kd=0.52uM
Enzymatic activity
Catalytic site (original residue number in PDB) C164 G233 E236 T237 T238 C343 L344 G345 E352 V383
Catalytic site (residue number reindexed from 1) C159 G228 E231 T232 T233 C338 L339 G340 E347 V378
Enzyme Commision number 1.14.15.28: cholest-4-en-3-one 26-monooxygenase [(25R)-3-oxocholest-4-en-26-oate forming].
Gene Ontology
Molecular Function
GO:0004497 monooxygenase activity
GO:0005506 iron ion binding
GO:0008395 steroid hydroxylase activity
GO:0016705 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
GO:0020037 heme binding
GO:0036199 cholest-4-en-3-one 26-monooxygenase activity
GO:0046872 metal ion binding
Biological Process
GO:0006707 cholesterol catabolic process
GO:0008203 cholesterol metabolic process
GO:0016042 lipid catabolic process

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Molecular Function
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Biological Process
External links
PDB RCSB:2yoo, PDBe:2yoo, PDBj:2yoo
PDBsum2yoo
PubMed23489718
UniProtA0R4Q6|CP142_MYCS2 Steroid C26-monooxygenase (Gene Name=cyp142)

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