Structure of PDB 7by9 Chain D Binding Site BS01

Receptor Information
>7by9 Chain D (length=311) Species: 1422 (Geobacillus stearothermophilus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AMKRKKISVIGAGFTGATTAFLLAQKELGDVVLVDIPQLENPTKGKALDM
LEASPVLGFDANIIGTSDYADTADSDIVVITAGIARKPGMSRDDLVTTNQ
KIMKQVTKEVVKYSPNCYIIVLTNPVDAMTYTVFKESGFPKNRVIGQSGV
LDTARFRTFVAEELNISVKDVTGFVLGGHGDDMVPLVRYSYAGGIPLEKL
IPKDRLDAIVERTRKGGGEIVNLLGNGSAYYAPAASLVEMVEAILKDQRR
ILPAIAYLEGEYGYEGIYLGVPTILGGNGIEKVIELELTEEEKAALAKSV
ESVKNVMRMLE
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 chain7by9 Chain D Residue 400 [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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PDB7by9 Structural analysis and reaction mechanism of malate dehydrogenase from Geobacillus stearothermophilus.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		G11 G13 F14 T15 D35 I36 T81 A82 Q105 L122 T123 N124 Q147 H179 P233
Binding residue
(residue number reindexed from 1)		G11 G13 F14 T15 D35 I36 T81 A82 Q105 L122 T123 N124 Q147 H179 P233
Annotation score4
Enzymatic activity
Enzyme Commision number 1.1.1.37: malate dehydrogenase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0003824 catalytic activity
GO:0004459 L-lactate dehydrogenase activity
GO:0016491 oxidoreductase activity
GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
GO:0030060 L-malate dehydrogenase (NAD+) activity
Biological Process
GO:0006089 lactate metabolic process
GO:0006090 pyruvate metabolic process
GO:0006099 tricarboxylic acid cycle
GO:0019752 carboxylic acid metabolic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:7by9, PDBe:7by9, PDBj:7by9
PDBsum7by9
PubMed33723609
UniProtA0A143T1U9

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