Structure of PDB 3vph Chain B Binding Site BS02

Receptor Information
>3vph Chain B (length=310) Species: 272 (Thermus caldophilus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKVGIVGSGMVGSATAYALALLGVAREVVLVDLDRKLAQAHAEDILHATP
FAHPVWVRAGSYGDLEGARAVVLAAGVAQRPGETRLQLLDRNAQVFAQVV
PRVLEAAPEAVLLVATNPVDVMTQVAYRLSALPPGRVVGSGTILDTARFR
ALLAEHLRVAPQSVHAYVLGEHGDSEVLVWSSAQVGGVPLLEFAEARGRA
LSPEDRARIDEGVRRAAYRIIEGKGATYYGIGAGLARLVRAILTDEKGVY
TVSAFTPEVEGVLEVSLSLPRILGAGGVEGTVYPSLSPEEREALRRSAEI
LKEAAFALGF
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 chain3vph Chain B Residue 403 [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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PDB3vph The core of allosteric motion in Thermus caldophilus L-lactate dehydrogenase.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		G29 M30 V31 D52 L53 A96 G97 V120 A136 T137 N138 S161 I251
Binding residue
(residue number reindexed from 1)		G9 M10 V11 D32 L33 A75 G76 V99 A115 T116 N117 S140 I231
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) R106 D166 R169 H193
Catalytic site (residue number reindexed from 1) R85 D145 R148 H172
Enzyme Commision number 1.1.1.27: L-lactate dehydrogenase.
Gene Ontology
Molecular Function
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
Biological Process
GO:0006089 lactate metabolic process
GO:0006090 pyruvate metabolic process
GO:0006096 glycolytic process
GO:0019752 carboxylic acid metabolic process
Cellular Component
GO:0005737 cytoplasm

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3vph, PDBe:3vph, PDBj:3vph
PDBsum3vph
PubMed25258319
UniProtP06150|LDH_THECA L-lactate dehydrogenase (Gene Name=ldh)

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