Structure of PDB 1drv Chain A Binding Site BS01

Receptor Information
>1drv Chain A (length=270) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ANIRVAIAGAGGRMGRQLIQAALALEGVQLGAALEREGSSLLGSDAGELA
GAGKTGVTVQSSLDAVKDDFDVFIDFTRPEGTLNHLAFCRQHGKGMVIGT
TGFDEAGKQAIRDAAADIAIVFAANFSVGVNVMLKLLEKAAKVMGDYTDI
EIIEAHHRHKVDAPSGTALAMGEAIAHALDKDLKDCAVYSREGHTGERVP
GTIGFATVRAGDIVGEHTAMFADIGERLEITHKASSRMTFANGAVRSALW
LSGKESGLFDMRDVLDLNNL
Ligand information
Ligand IDA3D
InChIInChI=1S/C22H28N6O14P2/c1-10(29)11-3-2-4-27(5-11)21-17(32)15(30)12(40-21)6-38-43(34,35)42-44(36,37)39-7-13-16(31)18(33)22(41-13)28-9-26-14-19(23)24-8-25-20(14)28/h2-5,8-9,12-13,15-18,21-22,30-33H,6-7H2,1H3,(H3-,23,24,25,34,35,36,37)/t12-,13-,15-,16-,17-,18-,21-,22-/m1/s1
InChIKeyKPVQNXLUPNWQHM-RBEMOOQDSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.5CC(=O)c1ccc[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)O)O
CACTVS 3.385CC(=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 1.7.5CC(=O)c1ccc[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)([O-])O[P@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)O)O
CACTVS 3.385CC(=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
FormulaC22 H28 N6 O14 P2
Name3-ACETYLPYRIDINE ADENINE DINUCLEOTIDE
ChEMBL
DrugBankDB03363
ZINC
PDB chain1drv Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1drv Interaction of pyridine nucleotide substrates with Escherichia coli dihydrodipicolinate reductase: thermodynamic and structural analysis of binary complexes.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		G12 G15 R16 M17 E38 F79 T80 R81 G84 G102 A127 F129 R240
Binding residue
(residue number reindexed from 1)		G9 G12 R13 M14 E35 F76 T77 R78 G81 G99 A124 F126 R237
Annotation score4
Binding affinityMOAD: Kd=0.29uM
PDBbind-CN: -logKd/Ki=6.54,Kd=0.29uM
Enzymatic activity
Catalytic site (original residue number in PDB) H159 K163
Catalytic site (residue number reindexed from 1) H156 K160
Enzyme Commision number 1.17.1.8: 4-hydroxy-tetrahydrodipicolinate reductase.
Gene Ontology
Molecular Function
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:0042802 identical protein binding
GO:0050661 NADP binding
GO:0051287 NAD binding
Biological Process
GO:0008652 amino acid biosynthetic 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:1drv, PDBe:1drv, PDBj:1drv
PDBsum1drv
PubMed8873595
UniProtP04036|DAPB_ECOLI 4-hydroxy-tetrahydrodipicolinate reductase (Gene Name=dapB)

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