Download MendeleyStructure-guided optimization of D-captopril for discovery of potent NDM-1 inhibitors
Ma, G., Wang, S., Wu, K., Zhang, W., Ahmad, A., Hao, Q., Lei, X., Zhang, H.(2020) Bioorg Med Chem 29
5ZIO
Crystal structure of NDM-1 in complex with L-captopril
- PDB DOI: https://doi.org/10.2210/pdb5ZIO/pdb
- Classification: HYDROLASE
- Organism(s): Klebsiella pneumoniae
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2018-03-16 Released: 2019-03-20
- Funding Organization(s): National Science Foundation (China)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 0.98 Å
- R-Value Free: 0.137
- R-Value Work: 0.123
- R-Value Observed: 0.124
Starting Model: experimental
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This is version 1.2 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Metallo-beta-lactamase type 2 | 242 | Klebsiella pneumoniae | Mutation(s): 0 Gene Names: blaNDM-1 EC: 3.5.2.6 |  | |
UniProt | |||||
Find proteins for C7C422 (Klebsiella pneumoniae) Explore C7C422 Go to UniProtKB: C7C422 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | C7C422 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| X8Z Query on X8Z | D [auth A] | L-CAPTOPRIL C9 H15 N O3 S FAKRSMQSSFJEIM-RQJHMYQMSA-N |  | ||
| ZN Query on ZN | B [auth A], C [auth A] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 0.98 Å
- R-Value Free: 0.137
- R-Value Work: 0.123
- R-Value Observed: 0.124
- Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 41.506 | α = 90 |
| b = 59.948 | β = 98.06 |
| c = 41.904 | γ = 90 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| DENZO | data reduction |
| SCALEPACK | data scaling |
| PDB_EXTRACT | data extraction |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Science Foundation (China) | China | 31670753 |
Revision History (Full details and data files)
- Version 1.0: 2019-03-20
Type: Initial release - Version 1.1: 2020-12-16
Changes: Database references - Version 1.2: 2023-11-22
Changes: Data collection, Database references, Refinement description
