Structure of PDB 2vle Chain A Binding Site BS01

Receptor Information
>2vle Chain A (length=494) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AVPAPNQQPEVFCNQIFINNEWHDAVSRKTFPTVNPSTGEVICQVAEGDK
EDVDKAVKAARAAFQLGSPWRRMDASHRGRLLNRLADLIERDRTYLAALE
TLDNGKPYVISYLVDLDMVLKCLRYYAGWADKYHGKTIPIDGDFFSYTRH
EPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPLTALYVAN
LIKEAGFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIGRVIQVA
AGSSNLKRVTLELGGKSPNIIMSDADMDWAVEQAHFALFFNQGQCCCAGS
RTFVQEDIYDEFVERSVARAKSRVVGNPFDSKTEQGPQVDETQFKKILGY
INTGKQEGAKLLCGGGIAADRGYFIQPTVFGDVQDGMTIAKEEIFGPVMQ
ILKFKTIEEVVGRANNSTYGLAAAVFTKDLDKANYLSQALQAGTVWVNCY
DVFGAQSPFGGYKMSGSGRELGEYGLQAYTEVKTVTVKVPQKNS
Ligand information
Ligand IDDZN
InChIInChI=1S/C21H20O9/c22-8-16-18(25)19(26)20(27)21(30-16)29-12-5-6-13-15(7-12)28-9-14(17(13)24)10-1-3-11(23)4-2-10/h1-7,9,16,18-23,25-27H,8H2/t16-,18-,19+,20-,21-/m1/s1
InChIKeyKYQZWONCHDNPDP-QNDFHXLGSA-N
SMILES
SoftwareSMILES
CACTVS 3.341OC[CH]1O[CH](Oc2ccc3C(=O)C(=COc3c2)c4ccc(O)cc4)[CH](O)[CH](O)[CH]1O
CACTVS 3.341OC[C@H]1O[C@@H](Oc2ccc3C(=O)C(=COc3c2)c4ccc(O)cc4)[C@H](O)[C@@H](O)[C@@H]1O
OpenEye OEToolkits 1.5.0c1cc(ccc1C2=COc3cc(ccc3C2=O)OC4C(C(C(C(O4)CO)O)O)O)O
ACDLabs 10.04O=C3c4ccc(OC1OC(C(O)C(O)C1O)CO)cc4OC=C3c2ccc(O)cc2
OpenEye OEToolkits 1.5.0c1cc(ccc1C2=COc3cc(ccc3C2=O)O[C@H]4[C@@H]([C@H]([C@@H]([C@H](O4)CO)O)O)O)O
FormulaC21 H20 O9
NameDAIDZIN;
4',7-DIHYDROXYISOFLAVONE;
7-O-B-D-GLUCOPYRANOSIDE
ChEMBLCHEMBL486422
DrugBankDB02115
ZINCZINC000004098610
PDB chain2vle Chain A Residue 1501 [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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PDB2vle Structure of Daidzin, a Naturally Occurring Anti-Alcohol-Addiction Agent, in Complex with Human Mitochondrial Aldehyde Dehydrogenase.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		M124 F170 M174 W177 F292 F296 C301 C302 D457 V458 F459
Binding residue
(residue number reindexed from 1)		M118 F164 M168 W171 F286 F290 C295 C296 D451 V452 F453
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.10,IC50=80nM
BindingDB: IC50=80nM
Enzymatic activity
Catalytic site (original residue number in PDB) N169 K192 E268 C302 E399 E476
Catalytic site (residue number reindexed from 1) N163 K186 E262 C296 E393 E470
Enzyme Commision number 1.2.1.3: aldehyde dehydrogenase (NAD(+)).
Gene Ontology
Molecular Function
GO:0004029 aldehyde dehydrogenase (NAD+) activity
GO:0004030 aldehyde dehydrogenase [NAD(P)+] activity
GO:0008957 phenylacetaldehyde dehydrogenase (NAD+) activity
GO:0009055 electron transfer activity
GO:0016491 oxidoreductase activity
GO:0016620 oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
GO:0051287 NAD binding
GO:0106435 carboxylesterase activity
Biological Process
GO:0005975 carbohydrate metabolic process
GO:0006066 alcohol metabolic process
GO:0006068 ethanol catabolic process
GO:0018937 nitroglycerin metabolic process
GO:0046185 aldehyde catabolic process
GO:1903179 regulation of dopamine biosynthetic process
GO:1905627 regulation of serotonin biosynthetic process
Cellular Component
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix
GO:0070062 extracellular exosome

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2vle, PDBe:2vle, PDBj:2vle
PDBsum2vle
PubMed18613661
UniProtP05091|ALDH2_HUMAN Aldehyde dehydrogenase, mitochondrial (Gene Name=ALDH2)

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