Structure of PDB 5d2r Chain A Binding Site BS04

Receptor Information
>5d2r Chain A (length=420) Species: 563041 (Helicobacter pylori G27) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SMEMIEKAPTDLEDRDKAPHLLLLAGIQGDEPGGFNATNLFLMHYSVLKG
LVEVVPVLNKPSMLRNHRGLYGDMNRKFAALDKKDPEYPTIQEIKSLIAK
PNIDAVLHLHDGGGYYRPVYVDAMLNPKRWGNCFIIDQDEVKGAKFPNLL
AFANNTIESINAHLLHPIEEYHLKNTRTAQGDTEMQKALTFYAINQKKSA
FANEASKELPLASRVFYHLQAIEGLLNQLNIPFKRDFELNPSSVHALIND
KSLWAKISSLPKIPLFNLRPRLNHFPLPHNTKIPQIPIESNAYIVGLVKN
KQEVFLKYGNKLMTRLSPFYIEFDPSLEEVKMQIDNKDQMVKIGSVVEVK
ESFYIHAMDNIRANVIGFSVSNENKPNEAGYTIRFKDFQKRFSLDKQERI
YRIEFYKNNAFSGMILVKFV
Ligand information
Ligand ID56W
InChIInChI=1S/C14H25N2O9P/c1-8(17)16-11(14(22)23)5-6-26(24,25)7-9(12(18)19)3-2-4-10(15)13(20)21/h9-11H,2-7,15H2,1H3,(H,16,17)(H,18,19)(H,20,21)(H,22,23)(H,24,25)/t9-,10+,11+/m0/s1
InChIKeyAWMPEAXWUINOES-HBNTYKKESA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC(=O)N[C@H](CC[P](O)(=O)C[C@H](CCC[C@@H](N)C(O)=O)C(O)=O)C(O)=O
ACDLabs 12.01C(CCC(C(=O)O)CP(CCC(C(=O)O)NC(=O)C)(=O)O)C(C(=O)O)N
OpenEye OEToolkits 1.9.2CC(=O)N[C@H](CCP(=O)(C[C@H](CCC[C@H](C(=O)O)N)C(=O)O)O)C(=O)O
OpenEye OEToolkits 1.9.2CC(=O)NC(CCP(=O)(CC(CCCC(C(=O)O)N)C(=O)O)O)C(=O)O
CACTVS 3.385CC(=O)N[CH](CC[P](O)(=O)C[CH](CCC[CH](N)C(O)=O)C(O)=O)C(O)=O
FormulaC14 H25 N2 O9 P
Name(2R,6R)-2-{[(R)-[(3R)-3-(acetylamino)-3-carboxypropyl](hydroxy)phosphoryl]methyl}-6-aminoheptanedioic acid
ChEMBL
DrugBank
ZINCZINC000263620252
PDB chain5d2r Chain A Residue 523 [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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PDB5d2r A Bacterial Cell Shape-Determining Inhibitor.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		Q46 E49 R86 N93 R94 H126 H128 G130 W148 M203 T208 A220 E222 K225
Binding residue
(residue number reindexed from 1)		Q28 E31 R68 N75 R76 H108 H110 G112 W130 M185 T190 A202 E204 K207
Annotation score1
Binding affinityMOAD: Ki=1.5uM
PDBbind-CN: -logKd/Ki=5.82,Ki=1.5uM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0046872 metal ion binding

View graph for
Molecular Function
External links
PDB RCSB:5d2r, PDBe:5d2r, PDBj:5d2r
PDBsum5d2r
PubMed26735022
UniProtB5ZAD9

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