Structure of PDB 3d4p Chain A Binding Site BS01

Receptor Information
>3d4p Chain A (length=307) Species: 93062 (Staphylococcus aureus subsp. aureus COL) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FKGNKVVLIGNGAVGSSYAFSLVNQSIVDELVIIDLDTEKVRGDVMDLKH
ATPYSPTTVRVKAGEYSDCHDADLVVICAGAAQKPTRLDLVSKNLKIFKS
IVGEVMASKFDGIFLVATNPVDILAYATWKFSGLPKERVIGSGTILDSAR
FRLLLSEAFDVAPRSVDAQIIGEHGDTELPVWSHANIAGQPLKTLLEQRP
EGKAQIEQIFVQTRDAAYDIIQAKGATYYGVAMGLARITEAIFRNEDAVL
TVSALLEGEYEEEDVYIGVPAVINRNGIRNVVEIPLNDEEQSKFAHSAKT
LKDIMAE
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 chain3d4p Chain A Residue 318 [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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PDB3d4p Crystal structure of Lactate Dehydrogenase from Staphylococcus Aureus complexed with NAD and pyruvate
Resolution1.8 Å
Binding residue
(original residue number in PDB)		G15 A16 V17 D38 L39 A82 G83 A122 N124 H179 V236
Binding residue
(residue number reindexed from 1)		G12 A13 V14 D35 L36 A79 G80 A117 N119 H174 V231
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) R92 D152 R155 H179
Catalytic site (residue number reindexed from 1) R87 D147 R150 H174
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3d4p, PDBe:3d4p, PDBj:3d4p
PDBsum3d4p
PubMed
UniProtQ5HJD7|LDH1_STAAC L-lactate dehydrogenase 1 (Gene Name=ldh1)

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