Structure of PDB 2qdt Chain A Binding Site BS03

Receptor Information
>2qdt Chain A (length=266) Species: 40324 (Stenotrophomonas maltophilia) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EVPLPQLRAYTVDASWLQPMAPLQIADHTWQIGTEDLTALLVQTPDGAVL
LDGGMPQMASHLLDNMKARGVTPRDLRLILLSHAHADHAGPVAELKRRTG
AKVAANAESAVLLARGGSDDLHFGDGITYPPANADRIVMDGEVITVGGIV
FTAHFMAGHTPGSTAWTWTDTRNGKPVRIAYADSLSAPGYQLQGNPRYPH
LIEDYRRSFATVRALPCDVLLTPHPGASNWDYAAGARAGAKALTCKAYAD
AAEQKFDGQLAKETAG
Ligand information
Ligand IDI38
InChIInChI=1S/C6H11NO3S/c1-4(6(9)10)7-5(8)2-3-11/h4,11H,2-3H2,1H3,(H,7,8)(H,9,10)/t4-/m1/s1
InChIKeyJIAFOCJABIEPNM-SCSAIBSYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C[C@H](C(=O)O)NC(=O)CCS
ACDLabs 10.04O=C(NC(C(=O)O)C)CCS
OpenEye OEToolkits 1.5.0CC(C(=O)O)NC(=O)CCS
CACTVS 3.341C[CH](NC(=O)CCS)C(O)=O
CACTVS 3.341C[C@@H](NC(=O)CCS)C(O)=O
FormulaC6 H11 N O3 S
NameN-(3-MERCAPTOPROPANOYL)-D-ALANINE
ChEMBL
DrugBankDB07939
ZINC
PDB chain2qdt Chain A Residue 501 [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]
PDB2qdt Structural basis for the broad-spectrum inhibition of metallo-beta-lactamases by thiols.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		D88 H160 S187 P189
Binding residue
(residue number reindexed from 1)		D87 H159 S186 P188
Annotation score1
Binding affinityMOAD: Ki=6.5uM
PDBbind-CN: -logKd/Ki=5.19,Ki=6.5uM
Enzymatic activity
Catalytic site (original residue number in PDB) H84 H86 D88 H89 H160 Y191 H225
Catalytic site (residue number reindexed from 1) H83 H85 D87 H88 H159 Y190 H224
Enzyme Commision number 3.5.2.6: beta-lactamase.
Gene Ontology
Molecular Function
GO:0008270 zinc ion binding
GO:0008800 beta-lactamase activity
GO:0016787 hydrolase activity
GO:0046872 metal ion binding
Biological Process
GO:0017001 antibiotic catabolic process
GO:0030655 beta-lactam antibiotic catabolic process
GO:0046677 response to antibiotic
Cellular Component
GO:0042597 periplasmic space

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2qdt, PDBe:2qdt, PDBj:2qdt
PDBsum2qdt
PubMed18563261
UniProtP52700|BLA1_STEMA Metallo-beta-lactamase L1 type 3

[Back to BioLiP]