Structure of PDB 1f06 Chain B Binding Site BS01

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 IDNDP
InChIInChI=1S/C21H30N7O17P3/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/h1,3-4,7-8,10-11,13-16,20-21,29-31H,2,5-6H2,(H2,23,32)(H,36,37)(H,38,39)(H2,22,24,25)(H2,33,34,35)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyACFIXJIJDZMPPO-NNYOXOHSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)N5C=CCC(=C5)C(=O)N)O)O)O)OP(=O)(O)O)N
CACTVS 3.341NC(=O)C1=CN(C=CC1)[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)C1=CN(C=CC1)[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 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)N5C=CCC(=C5)C(=O)N)O)O)O)OP(=O)(O)O)N
FormulaC21 H30 N7 O17 P3
NameNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
ChEMBLCHEMBL407009
DrugBankDB02338
ZINCZINC000008215411
PDB chain1f06 Chain B Residue 901 [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)		G510 G512 N513 L514 S535 R536 R537 C565 S568 T588 D590 T617 G618 W619 Q650 G651 T774
Binding residue
(residue number reindexed from 1)		G10 G12 N13 L14 S35 R36 R37 C65 S68 T88 D90 T117 G118 W119 Q150 G151 T274
Annotation score4
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]