Structure of PDB 4e5m Chain A Binding Site BS01

Receptor Information
>4e5m Chain A (length=329) Species: 316 (Stutzerimonas stutzeri) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MLPKLVITHRVHEEILQLLAPHCELITNQTDSTLTREEILRRCRDAQAMM
AFMPDRVDADFLQACPELRVIGCALKGFDNFDVDACTARGVWLTFVPDLL
TVPTAELAIGLAVGLGRHLRAADAFVRSGQFRGWQPRFYGTGLDNATVGF
LGMGAIGLAMADRLQGWGATLQYHARKALDTQTEQRLGLRQVACSELFAS
SDFILLALPLNADTLHLVNAELLALVRPGALLVNPCRGSVVDEAAVLAAL
ERGQLGGYAADVFEMEDWARADRPQQIDPALLAHPNTLFTPHIGSAVRAV
RLEIERCAAQNILQALAGERPINAVNRLP
Ligand information
Ligand IDNAP
InChIInChI=1S/C21H28N7O17P3/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/h1-4,7-8,10-11,13-16,20-21,29-31H,5-6H2,(H7-,22,23,24,25,32,33,34,35,36,37,38,39)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyXJLXINKUBYWONI-NNYOXOHSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)OP(=O)(O)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[P](O)(O)=O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
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[P](O)(O)=O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]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)OP(=O)(O)O)O)O)O)C(=O)N
FormulaC21 H28 N7 O17 P3
NameNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE;
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
ChEMBLCHEMBL295069
DrugBankDB03461
ZINC
PDB chain4e5m Chain A Residue 800 [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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PDB4e5m Crystal structures of phosphite dehydrogenase provide insights into nicotinamide cofactor regeneration.
Resolution1.85 Å
Binding residue
(original residue number in PDB)		K76 L100 T104 G154 A155 I156 R176 L208 P209 T214 P235 C236 R237 H292 G294
Binding residue
(residue number reindexed from 1)		K76 L100 T104 G154 A155 I156 R176 L208 P209 T214 P235 C236 R237 H292 G294
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) L100 R237 D261 E266 H292
Catalytic site (residue number reindexed from 1) L100 R237 D261 E266 H292
Enzyme Commision number 1.20.1.1: phosphonate dehydrogenase.
Gene Ontology
Molecular Function
GO:0008465 hydroxypyruvate reductase (NADH) activity
GO:0016491 oxidoreductase activity
GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
GO:0030267 glyoxylate reductase (NADPH) activity
GO:0050609 phosphonate dehydrogenase activity
GO:0051287 NAD binding
Cellular Component
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Cellular Component
External links
PDB RCSB:4e5m, PDBe:4e5m, PDBj:4e5m
PDBsum4e5m
PubMed22564171
UniProtO69054|PTXD_STUST Phosphonate dehydrogenase (Gene Name=ptxD)

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