Structure of PDB 1f06 Chain B Binding Site BS02

Receptor Information
>1f06 Chain B (length=320) Species: 1718 (Corynebacterium glutamicum) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MTNIRVAIVGYGNLGRSVEKLIAKQPDMDLVGIFSRRATLDTKTPVFDVA
DVDKHADDVDVLFLCMGSATDIPEQAPKFAQFACTVDTYDNHRDIPRHRQ
VMNEAATAAGNVALVSTGWDPGMFSINRVYAAAVLAEHQQHTFWGPGLSQ
GHSDALRRIPGVQKAVQYTLPSEDALEKARRGEAGDLTGKQTHKRQCFVV
ADAADHERIENDIRTMPDYFVGYEVEVNFIDEATFDSEHTGMPHGGHVIT
TGDTGGFNHTVEYILKLDRNPDFTASSQIAFGRAAHRMKQQGQSGAFTVL
EVAPYLLSPENLDDLIARDV
Ligand information
Ligand ID2NP
InChIInChI=1S/C8H13NO4/c1-5(7(10)11)3-2-4-6(9)8(12)13/h6H,1-4,9H2,(H,10,11)(H,12,13)/t6-/m0/s1
InChIKeySGAIRWMSXVAPOO-LURJTMIESA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C=C(CCCC(C(=O)O)N)C(=O)O
OpenEye OEToolkits 1.5.0C=C(CCC[C@@H](C(=O)O)N)C(=O)O
CACTVS 3.341N[CH](CCCC(=C)C(O)=O)C(O)=O
CACTVS 3.341N[C@@H](CCCC(=C)C(O)=O)C(O)=O
ACDLabs 10.04O=C(O)/C(=C)CCCC(N)C(=O)O
FormulaC8 H13 N O4
NameL-2-AMINO-6-METHYLENE-PIMELIC ACID
ChEMBL
DrugBankDB02892
ZINCZINC000002046788
PDB chain1f06 Chain B Residue 950 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB1f06 The three-dimensional structure of the ternary complex of Corynebacterium glutamicum diaminopimelate dehydrogenase-NADPH-L-2-amino-6-methylene-pimelate.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		D590 W619 W644 S649 Q650 G651 H652 T669 R695 H744 N770
Binding residue
(residue number reindexed from 1)		D90 W119 W144 S149 Q150 G151 H152 T169 R195 H244 N270
Annotation score3
Binding affinityMOAD: Ki=5uM
Enzymatic activity
Enzyme Commision number 1.4.1.16: diaminopimelate dehydrogenase.
Gene Ontology
Molecular Function
GO:0016491 oxidoreductase activity
GO:0047850 diaminopimelate dehydrogenase activity
Biological Process
GO:0009085 lysine biosynthetic process
GO:0009089 lysine biosynthetic process via diaminopimelate
GO:0019877 diaminopimelate biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:1f06, PDBe:1f06, PDBj:1f06
PDBsum1f06
PubMed11106178
UniProtP04964|DAPDH_CORGL Meso-diaminopimelate D-dehydrogenase (Gene Name=ddh)

[Back to BioLiP]