Macromolecule Content

Total Structure Weight: 25.98 kDa
Atom Count: 2,059
Modelled Residue Count: 228
Deposited Residue Count: 242
Unique protein chains: 1

5ZIO

Crystal structure of NDM-1 in complex with L-captopril

PDB DOI: 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
Deposition Author(s): Zhang, H., Hao, Q.
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

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structure-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

DOI: 10.1016/j.bmc.2020.115902

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	A	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
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
X8Z Query on X8Z Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	L-CAPTOPRIL C₉ H₁₅ N O₃ S FAKRSMQSSFJEIM-RQJHMYQMSA-N		Ligand Interaction
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A]	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Ligand Interaction

Binding Affinity Annotations
ID	Source	Binding Affinity
X8Z	BindingDB: 5ZIO	Kd: min: 1.40e+4, max: 1.41e+4 (nM) from 2 assay(s)
X8Z	BindingDB: 5ZIO	IC50: min: 4.98e+4, max: 5.01e+4 (nM) from 2 assay(s)

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 Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2019-03-20

Deposition Author(s):

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.