Structure of PDB 2pd6 Chain C Binding Site BS01

Receptor Information
>2pd6 Chain C (length=237) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ALALVTGAGSGIGRAVSVRLAGEGATVAACDLDRAAAQETVRLLNHAAFQ
ADVSEARAARCLLEQVQACFSRPPSVVVSCAGITQDEFLLHMSEDDWDKV
IAVNLKGTFLVTQAAAQALVSNGCRGSIINISSIVGKVGNVGQTNYAASK
AGVIGLTQTAARELGRHGIRCNSVLPGFIATPMTQKVPQKVVDKITEMIP
MGHLGDPEDVADVVAFLASEDSGYITGTSVEVTGGLF
Ligand information
Ligand IDNAD
InChIInChI=1S/C21H27N7O14P2/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33/h1-4,7-8,10-11,13-16,20-21,29-32H,5-6H2,(H5-,22,23,24,25,33,34,35,36,37)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyBAWFJGJZGIEFAR-NNYOXOHSSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC(=O)c1ccc[n+](c1)[C@@H]2O[C@H](CO[P]([O-])(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
CACTVS 3.341NC(=O)c1ccc[n+](c1)[CH]2O[CH](CO[P]([O-])(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)([O-])O[P@@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
FormulaC21 H27 N7 O14 P2
NameNICOTINAMIDE-ADENINE-DINUCLEOTIDE
ChEMBLCHEMBL1234613
DrugBankDB14128
ZINC
PDB chain2pd6 Chain C Residue 3 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2pd6 Structure of human hydroxysteroid dehydrogenase type 8, HSD17B8
Resolution2.0 Å
Binding residue
(original residue number in PDB)		G18 S21 G22 I23 D42 L43 A74 D75 V76 C103 A104 I154 S156 Y169 K173 P199 I202 T204 M206 T207
Binding residue
(residue number reindexed from 1)		G7 S10 G11 I12 D31 L32 A51 D52 V53 C80 A81 I131 S133 Y146 K150 P176 I179 T181 M183 T184
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) G22 S156 Y169 K173
Catalytic site (residue number reindexed from 1) G11 S133 Y146 K150
Enzyme Commision number 1.1.1.239: 3alpha-(17beta)-hydroxysteroid dehydrogenase (NAD(+)).
1.1.1.62: 17beta-estradiol 17-dehydrogenase.
1.1.1.n12: (3R)-hydroxyacyl-CoA dehydrogenase.
Gene Ontology
Molecular Function
GO:0004303 estradiol 17-beta-dehydrogenase [NAD(P)+] activity
GO:0005515 protein binding
GO:0016491 oxidoreductase activity
GO:0047035 testosterone dehydrogenase (NAD+) activity
GO:0070404 NADH binding
GO:0106386 (3R)-hydroxyacyl-CoA dehydrogenase (NAD+) activity
Biological Process
GO:0006633 fatty acid biosynthetic process
GO:0006694 steroid biosynthetic process
GO:0006703 estrogen biosynthetic process
GO:0008209 androgen metabolic process
GO:0008210 estrogen metabolic process
GO:0051290 protein heterotetramerization
Cellular Component
GO:0005739 mitochondrion
GO:0005740 mitochondrial envelope
GO:0005759 mitochondrial matrix
GO:0005886 plasma membrane
GO:0016020 membrane
GO:1990204 oxidoreductase complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2pd6, PDBe:2pd6, PDBj:2pd6
PDBsum2pd6
PubMed
UniProtQ92506|DHB8_HUMAN (3R)-3-hydroxyacyl-CoA dehydrogenase (Gene Name=HSD17B8)

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