7DUY

Crystal structure of VIM-2 MBL in complex with 1-(2-(1H-1,2,3-triazol-1-yl)ethyl)-1H-imidazole-2-carboxylic acid

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.189 

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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history. 


Literature

Discovery and Structural Basis of 1H-Imidazole-2-Carboxylic Acid Derivatives as Metallo-beta-Lactamase Inhibitors for Carbapenem-Resistant Gram-Negative Bacterial Infections

Yan, Y.-H., Li, W.-F., Yang, L.-L., Li, C., Zhu, K.-R., Deng, J., Dai, Q.-Q., Wang, Z.-L., Wu, Y., Li, G.-B.

To be published.

Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-lactamase class B VIM-2A231Pseudomonas aeruginosaMutation(s): 0 
Gene Names: blaVIM-2, bla vim-2, bla-VIM-2, blasVIM-2, blaVIM2, VIM-2, vim-2, IPC669_36195
UniProt
Find proteins for Q9K2N0 (Pseudomonas aeruginosa)
Explore Q9K2N0 
Go to UniProtKB:  Q9K2N0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9K2N0
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HLL (Subject of Investigation/LOI)
Query on HLL
Download Ideal Coordinates CCD File 
D [auth A]1-[2-(1,2,3-triazol-1-yl)ethyl]imidazole-2-carboxylic acid
C8 H9 N5 O2
BICABFBIPKZSEC-UHFFFAOYSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.189 
  • Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.038α = 90
b = 64.223β = 90
c = 91.554γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

  • Deposited Date: 2021-01-12 
  • Released Date: 2022-01-19 
    • Deposition Author(s): Li, G.-B., Yan, Y.-H.
Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China81874291
National Natural Science Foundation of China (NSFC)China81502989
National Natural Science Foundation of China (NSFC)China82073698

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-19
    Type: Initial release