Structure of PDB 3d3f Chain B Binding Site BS01

Receptor Information
>3d3f Chain B (length=275) Species: 1423 (Bacillus subtilis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PTSLKDTVKLHNGVEMPWFGLGVFKVENGNEATESVKAAIKNGYRSIDTA
AIYKNEEGVGIGIKESGVAREELFITSKVWNEDQGYETTLAAFEKSLERL
QLDYLDLYLIHWPGKDKYKDTWRALEKLYKDGKIRAIGVSNFQVHHLEEL
LKDAEIKPMVNQVEFHPRLTQKELRDYCKGQGIQLEAWSPLMQGQLLDNE
VLTQIAEKHNKSVAQVILRWDLQHGVVTIPKSIKEHRIIENADIFDFELS
QEDMDKIDALNKDERVGPNPDELLF
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 chain3d3f Chain B Residue 1 [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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PDB3d3f Structural and biochemical analyses of YvgN and YtbE from Bacillus subtilis
Resolution2.4 Å
Binding residue
(original residue number in PDB)		G23 V24 F25 D49 Y54 H112 N142 Q163 W189 S190 P191 L192 Q194 L198 I230 K232 S233 I234 K235 R238 N242
Binding residue
(residue number reindexed from 1)		G22 V23 F24 D48 Y53 H111 N141 Q162 W188 S189 P190 L191 Q193 L197 I229 K231 S232 I233 K234 R237 N241
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) D49 Y54 K79 H112
Catalytic site (residue number reindexed from 1) D48 Y53 K78 H111
Enzyme Commision number 1.1.1.-
1.1.1.283: methylglyoxal reductase (NADPH).
Gene Ontology
Molecular Function
GO:0004033 aldo-keto reductase (NADPH) activity
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

View graph for
Molecular Function
External links
PDB RCSB:3d3f, PDBe:3d3f, PDBj:3d3f
PDBsum3d3f
PubMed19585557
UniProtO32210|GR_BACSU Glyoxal reductase (Gene Name=yvgN)

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