Structure of PDB 1e6w Chain D Binding Site BS01

Receptor Information
>1e6w Chain D (length=255) Species: 10116 (Rattus norvegicus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SVKGLVAVITGGASGLGLSTAKRLVGQGATAVLLDVPNSEGETEAKKLGG
NCIFAPANVTSEKEVQAALTLAKEKFGRIDVAVNCAGIAVAIKTYHEKKN
QVHTLEDFQRVINVNLIGTFNVIRLVAGVMGQNEPDQGGQRGVIINTASV
AAFEGQVGQAAYSASKGGIVGMTLPIARDLAPIGIRVVTIAPGLFATPLL
TTLPDKVRNFLASQVPFPSRLGDPAEYAHLVQMVIENPFLNGEVIRLDGA
IRMQP
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 chain1e6w Chain D Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB1e6w Recognition of Structurally Diverse Substrates by Type II 3-Hydroxyacyl-Coa Dehydrogenase (Hadh II) Amyloid-Beta Binding Alcohol Dehydrogenase (Abad)
Resolution1.7 Å
Binding residue
(original residue number in PDB)		G17 S20 G21 L22 D41 V42 N64 V65 C91 A92 G93 T153 Y168 K172 P198 L200 F201 T203 L205
Binding residue
(residue number reindexed from 1)		G11 S14 G15 L16 D35 V36 N58 V59 C85 A86 G87 T147 Y162 K166 P192 L194 F195 T197 L199
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) G21 N121 T153 S155 Y168 K172 F201
Catalytic site (residue number reindexed from 1) G15 N115 T147 S149 Y162 K166 F195
Enzyme Commision number 1.1.1.159: 7alpha-hydroxysteroid dehydrogenase.
1.1.1.178: 3-hydroxy-2-methylbutyryl-CoA dehydrogenase.
1.1.1.239: 3alpha-(17beta)-hydroxysteroid dehydrogenase (NAD(+)).
1.1.1.35: 3-hydroxyacyl-CoA dehydrogenase.
1.1.1.53: 3alpha(or 20beta)-hydroxysteroid dehydrogenase.
1.1.1.62: 17beta-estradiol 17-dehydrogenase.
Gene Ontology
Molecular Function
GO:0000049 tRNA binding
GO:0001540 amyloid-beta binding
GO:0003857 3-hydroxyacyl-CoA dehydrogenase activity
GO:0004303 estradiol 17-beta-dehydrogenase [NAD(P)+] activity
GO:0005496 steroid binding
GO:0008709 cholate 7-alpha-dehydrogenase activity
GO:0016491 oxidoreductase activity
GO:0018454 acetoacetyl-CoA reductase activity
GO:0030283 testosterone dehydrogenase [NAD(P)+] activity
GO:0030331 nuclear estrogen receptor binding
GO:0042802 identical protein binding
GO:0044594 17-beta-hydroxysteroid dehydrogenase (NAD+) activity
GO:0047015 3-hydroxy-2-methylbutyryl-CoA dehydrogenase activity
GO:0047035 testosterone dehydrogenase (NAD+) activity
GO:0047044 androstan-3-alpha,17-beta-diol dehydrogenase activity
GO:0051287 NAD binding
GO:0106281 chenodeoxycholate 7-alpha-dehydrogenase (NAD+) activity
GO:0106282 isoursodeoxycholate 7-beta-dehydrogenase (NAD+) activity
GO:0106283 ursodeoxycholate 7-beta-dehydrogenase (NAD+) activity
Biological Process
GO:0006550 isoleucine catabolic process
GO:0006631 fatty acid metabolic process
GO:0006635 fatty acid beta-oxidation
GO:0006699 bile acid biosynthetic process
GO:0007005 mitochondrion organization
GO:0008033 tRNA processing
GO:0008202 steroid metabolic process
GO:0008207 C21-steroid hormone metabolic process
GO:0008209 androgen metabolic process
GO:0008210 estrogen metabolic process
GO:0008584 male gonad development
GO:0033327 Leydig cell differentiation
GO:0051289 protein homotetramerization
GO:0062173 brexanolone metabolic process
GO:0070901 mitochondrial tRNA methylation
GO:0097745 mitochondrial tRNA 5'-end processing
GO:1990180 mitochondrial tRNA 3'-end processing
Cellular Component
GO:0005739 mitochondrion
GO:0005783 endoplasmic reticulum
GO:0030678 mitochondrial ribonuclease P complex
GO:0042645 mitochondrial nucleoid
GO:0043527 tRNA methyltransferase complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1e6w, PDBe:1e6w, PDBj:1e6w
PDBsum1e6w
PubMed11023795
UniProtO70351|HCD2_RAT 3-hydroxyacyl-CoA dehydrogenase type-2 (Gene Name=Hsd17b10)

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