Structure of PDB 3td4 Chain A Binding Site BS01

Receptor Information
>3td4 Chain A (length=122) Species: 470 (Acinetobacter baumannii) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SHMELTEDLNMELRVFFDTNKSNIKDQYKPEIAKVAEKLSEYPNATARIE
GHTDNTGPRKLNERLSLARANSVKSALVNEYNVDASRLSTQGFAWDQPIA
DNKTKEGRAMNRRVFATITGSR
Ligand information
Ligand IDAPI
InChIInChI=1S/C7H14N2O4/c8-4(6(10)11)2-1-3-5(9)7(12)13/h4-5H,1-3,8-9H2,(H,10,11)(H,12,13)/t4-,5+
InChIKeyGMKMEZVLHJARHF-SYDPRGILSA-N
SMILES
SoftwareSMILES
CACTVS 3.370N[CH](CCC[CH](N)C(O)=O)C(O)=O
OpenEye OEToolkits 1.7.2C(C[C@H](C(=O)O)N)C[C@@H](C(=O)O)N
OpenEye OEToolkits 1.7.2C(CC(C(=O)O)N)CC(C(=O)O)N
CACTVS 3.370N[C@@H](CCC[C@@H](N)C(O)=O)C(O)=O
ACDLabs 12.01O=C(O)C(N)CCCC(C(=O)O)N
FormulaC7 H14 N2 O4
Name2,6-DIAMINOPIMELIC ACID
ChEMBLCHEMBL415306
DrugBank
ZINCZINC000001532722
PDB chain3td4 Chain A Residue 401 [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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PDB3td4 Mechanism of anchoring of OmpA protein to the cell wall peptidoglycan of the gram-negative bacterial outer membrane
Resolution1.79 Å
Binding residue
(original residue number in PDB)		T236 N237 T270 D271 T273 G274 N279 L282 R286 R329
Binding residue
(residue number reindexed from 1)		T19 N20 T53 D54 T56 G57 N62 L65 R69 R112
Annotation score1
Binding affinityMOAD: Kd=2.2uM
PDBbind-CN: -logKd/Ki=5.66,Kd=2.2uM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology

View graph for
Cellular Component
External links
PDB RCSB:3td4, PDBe:3td4, PDBj:3td4
PDBsum3td4
PubMed21965596
UniProtQ6RYW5|OMP38_ACIB2 Outer membrane protein Omp38 (Gene Name=omp38)

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