Structure of PDB 3ejx Chain D Binding Site BS01

Receptor Information
>3ejx Chain D (length=301) Species: 3702 (Arabidopsis thaliana) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EKFSPASFLDKKETGVLHFVKYHGLGNDFILVDNRDSSEPKITQEQAAKL
CDRNFGVGADGVIFAMPGVNGTDYAMRIFNSDGSEPEMCGNGVRCFARFI
AELENLQGKHSFTIHTGAGLIVPEIQDDGQVKVDMGTPILKAQDVPTKLS
GNKGEAVVEAELVVDGVSWNVTCVSMGNPHCITFGKKGGPNLKVDDLNLP
EIGPKFEHHEMFPARTNTEFVEVLSRSHLKMRVWERGAGATLACGTGACA
LVVAAVLEGRADRKCTVDLPGGPLEIEWKQEDNHIYMTGPAEAVFYGSAL
L
Ligand information
Ligand IDZDP
InChIInChI=1S/C8H16N2O4/c1-8(10,7(13)14)4-2-3-5(9)6(11)12/h5H,2-4,9-10H2,1H3,(H,11,12)(H,13,14)/t5-,8-/m0/s1
InChIKeyTVZGBXIJPFGQBJ-XNCJUZBTSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.5C[C@](CCC[C@@H](C(=O)O)N)(C(=O)O)N
CACTVS 3.385C[C](N)(CCC[CH](N)C(O)=O)C(O)=O
OpenEye OEToolkits 1.7.5CC(CCCC(C(=O)O)N)(C(=O)O)N
CACTVS 3.385C[C@](N)(CCC[C@H](N)C(O)=O)C(O)=O
ACDLabs 10.04O=C(O)C(N)(CCCC(N)C(=O)O)C
FormulaC8 H16 N2 O4
Name(2S,6S)-2,6-DIAMINO-2-METHYLHEPTANEDIOIC ACID
ChEMBL
DrugBank
ZINC
PDB chain3ejx Chain D Residue 500 [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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PDB3ejx Crystal structure of diaminopimelate epimerase from Arabidopsis thaliana, an amino acid racemase critical for L-lysine biosynthesis.
Resolution1.95 Å
Binding residue
(original residue number in PDB)		N37 F39 N90 P96 C99 G100 N101 N188 N227 E245 R246 C254 G255 T256
Binding residue
(residue number reindexed from 1)		N27 F29 N80 P86 C89 G90 N91 N178 N217 E235 R236 C244 G245 T246
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) C99 H190 E245 C254 G257
Catalytic site (residue number reindexed from 1) C89 H180 E235 C244 G247
Enzyme Commision number 5.1.1.7: diaminopimelate epimerase.
Gene Ontology
Molecular Function
GO:0008837 diaminopimelate epimerase activity
Biological Process
GO:0009089 lysine biosynthetic process via diaminopimelate
Cellular Component
GO:0005737 cytoplasm

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3ejx, PDBe:3ejx, PDBj:3ejx
PDBsum3ejx
PubMed19013471
UniProtQ9LFG2|DAPF_ARATH Diaminopimelate epimerase, chloroplastic (Gene Name=DAPF)

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