Structure of PDB 5z2f Chain A Binding Site BS01

Receptor Information
>5z2f Chain A (length=265) Species: 1231057 (Paenisporosarcina sp. TG-14) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MMIRVAIGGPRGKMGQEAVHTVMNNENMELVAVLDHKDIGDLLSESPNFP
ASYEVPVFLNLESLIVTIKPDVFLDLTTPHQVFEHTMLCLQNNVRPVIGT
TGFTDEQLQQCTILAEVNKLGCIVAPNFAIGAVLMMKFASLAAAYFPDVE
IIEMHHDQKLDAPSGTAYKTAQMIAEVRPSHKQGHPNEKETLEGARGASY
DGIPIHSVRLPGLIAHQQILFGGEGQLFTLRHDSYNRQSFMSGVTFSINQ
VMEIKELVYGLENIL
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 chain5z2f Chain A Residue 301 [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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PDB5z2f Crystal structure of dihydrodipicolinate reductase (PaDHDPR) from Paenisporosarcina sp. TG-14: structural basis for NADPH preference as a cofactor
Resolution2.1 Å
Binding residue
(original residue number in PDB)		R10 G11 K12 M13 D34 H35 K36 L75 T76 G98 T99 T100 P125 N126 F127
Binding residue
(residue number reindexed from 1)		R11 G12 K13 M14 D35 H36 K37 L76 T77 G99 T100 T101 P126 N127 F128
Annotation score4
Enzymatic activity
Enzyme Commision number 1.17.1.8: 4-hydroxy-tetrahydrodipicolinate reductase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0008839 4-hydroxy-tetrahydrodipicolinate reductase
GO:0016491 oxidoreductase activity
GO:0016726 oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor
GO:0050661 NADP binding
GO:0051287 NAD binding
Biological Process
GO:0009085 lysine biosynthetic process
GO:0009089 lysine biosynthetic process via diaminopimelate
GO:0019877 diaminopimelate biosynthetic process
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5z2f, PDBe:5z2f, PDBj:5z2f
PDBsum5z2f
PubMed29786696
UniProtA0A3B6UER2

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