Structure of PDB 4pvd Chain A Binding Site BS01

Receptor Information
>4pvd Chain A (length=342) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MSVFVSGANGFIAQHIVDLLLKEDYKVIGSARSQEKAENLTEAFGNNPKF
SMEVVPDISKLDAFDHVFQKHGKDIKIVLHTASPFCFDITDSERDLLIPA
VNGVKGILHSIKKYAADSVERVVLTSSYAAVFDMAKENDKSLTFNEESWN
PATWESCQSDPVNAYCGSKKFAEKAAWEFLEENRDSVKFELTAVNPVYVF
GPQMFDKDVKKHLNTSCELVNSLMHLSPEDKIPELFGGYIDVRDVAKAHL
VAFQKRETIGQRLIVSEARFTMQDVLDILNEDFPVLKGNIPVGKPGSGAT
HNTLGATLDNKKSKKLLGFKFRNLKETIDDTASQILKFEGRI
Ligand information
Ligand IDNDP
InChIInChI=1S/C21H30N7O17P3/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(44-46(33,34)35)14(30)11(43-21)6-41-48(38,39)45-47(36,37)40-5-10-13(29)15(31)20(42-10)27-3-1-2-9(4-27)18(23)32/h1,3-4,7-8,10-11,13-16,20-21,29-31H,2,5-6H2,(H2,23,32)(H,36,37)(H,38,39)(H2,22,24,25)(H2,33,34,35)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyACFIXJIJDZMPPO-NNYOXOHSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5C=CCC(=C5)C(=O)N)O)O)O)OP(=O)(O)O)N
CACTVS 3.341NC(=O)C1=CN(C=CC1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O[P](O)(O)=O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
CACTVS 3.341NC(=O)C1=CN(C=CC1)[C@@H]2O[C@H](CO[P@@](O)(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O[P](O)(O)=O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)N5C=CCC(=C5)C(=O)N)O)O)O)OP(=O)(O)O)N
FormulaC21 H30 N7 O17 P3
NameNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
ChEMBLCHEMBL407009
DrugBankDB02338
ZINCZINC000008215411
PDB chain4pvd Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4pvd Structural insights into the cofactor-assisted substrate recognition of yeast methylglyoxal/isovaleraldehyde reductase Gre2
Resolution2.4 Å
Binding residue
(original residue number in PDB)		G7 N9 G10 F11 I12 R32 K36 D57 I58 T81 S83 P84 F85 T125 S127 K169 P196 V197 Y198 V199 S216
Binding residue
(residue number reindexed from 1)		G7 N9 G10 F11 I12 R32 K36 D57 I58 T81 S83 P84 F85 T125 S127 K169 P196 V197 Y198 V199 S216
Annotation score4
Enzymatic activity
Enzyme Commision number 1.1.1.265: 3-methylbutanal reductase.
1.1.1.283: methylglyoxal reductase (NADPH).
Gene Ontology
Molecular Function
GO:0016491 oxidoreductase activity
GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
GO:0043892 methylglyoxal reductase (NADPH) activity
GO:0046568 3-methylbutanal reductase [NAD(P)H] activity
GO:0052675 3-methylbutanal reductase (NADPH) activity
GO:0052676 3-methylbutanal reductase (NADH) activity
Biological Process
GO:0006694 steroid biosynthetic process
GO:0008204 ergosterol metabolic process
GO:0030447 filamentous growth
Cellular Component
GO:0005634 nucleus
GO:0005737 cytoplasm

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4pvd, PDBe:4pvd, PDBj:4pvd
PDBsum4pvd
PubMed24879127
UniProtQ12068|GRE2_YEAST NADPH-dependent methylglyoxal reductase GRE2 (Gene Name=GRE2)

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