Structure of PDB 5f1u Chain A Binding Site BS01

Receptor Information
>5f1u Chain A (length=297) Species: 197 (Campylobacter jejuni) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DKNIIIGAMTALITPFKNGKVDEQSYARLIKRQIENGIDAVVPVGTTGES
ATLTHEEHRTCIEIAVETCKGTKVKVLAGAGSNATHEAVGLAKFAKEHGA
DGILSVAPFYNKPTQQGLYEHYKAIAQSVDIPVLLYNVPGRTGCEISTDT
IIKLFRDCENIYGVKEASGNIDKCVDLLAHEPRMMLISGEDAINYPILSN
GGKGVISVTSNLLPDMISALTHFALDENYKEAKKINDELYNINKILFCES
NPIPIKTAMYLAGLIESLEFRLPLCSPSKENFAKIEEVMKKYKIKGF
Ligand information
Ligand ID3VN
InChIInChI=1S/C14H30N4O4/c15-9-3-1-5-13(17,11(19)20)7-8-14(18,12(21)22)6-2-4-10-16/h1-10,15-18H2,(H,19,20)(H,21,22)/t13-,14-/m1/s1
InChIKeyXYUHPPVEDOOPDE-ZIAGYGMSSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C(O)C(N)(CCC(N)(C(=O)O)CCCCN)CCCCN
CACTVS 3.385NCCCC[C@@](N)(CC[C@](N)(CCCCN)C(O)=O)C(O)=O
OpenEye OEToolkits 1.7.6C(CCN)CC(CCC(CCCCN)(C(=O)O)N)(C(=O)O)N
CACTVS 3.385NCCCC[C](N)(CC[C](N)(CCCCN)C(O)=O)C(O)=O
OpenEye OEToolkits 1.7.6C(CCN)C[C@@](CC[C@](CCCCN)(C(=O)O)N)(C(=O)O)N
FormulaC14 H30 N4 O4
Name(2R,5R)-2,5-diamino-2,5-bis(4-aminobutyl)hexanedioic acid;
bis-Lysine
ChEMBLCHEMBL4516644
DrugBank
ZINCZINC000263621249
PDB chain5f1u 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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PDB5f1u Biomimetic Design Results in a Potent Allosteric Inhibitor of Dihydrodipicolinate Synthase from Campylobacter jejuni.
Resolution2.35 Å
Binding residue
(original residue number in PDB)		S51 A52 L54 H59 N84 E88
Binding residue
(residue number reindexed from 1)		S50 A51 L53 H58 N83 E87
Annotation score1
Binding affinityMOAD: ic50=400nM
PDBbind-CN: -logKd/Ki=6.40,IC50=400nM
Enzymatic activity
Catalytic site (original residue number in PDB) T47 Y111 Y137 R142 K166 I207
Catalytic site (residue number reindexed from 1) T46 Y110 Y136 R141 K165 I206
Enzyme Commision number 4.3.3.7: 4-hydroxy-tetrahydrodipicolinate synthase.
Gene Ontology
Molecular Function
GO:0008840 4-hydroxy-tetrahydrodipicolinate synthase activity
GO:0016829 lyase activity
Biological Process
GO:0009085 lysine biosynthetic process
GO:0009089 lysine biosynthetic process via diaminopimelate
GO:0019877 diaminopimelate biosynthetic process
GO:0044281 small molecule metabolic 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:5f1u, PDBe:5f1u, PDBj:5f1u
PDBsum5f1u
PubMed26836694
UniProtQ9PPB4|DAPA_CAMJE 4-hydroxy-tetrahydrodipicolinate synthase (Gene Name=dapA)

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