3KID

The Crystal Structures of 2-Aminobenzothiazole-based Inhibitors in Complexes with Urokinase-type Plasminogen Activator

PDB DOI: https://doi.org/10.2210/pdb3KID/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Komagataella pastoris
Mutation(s): Yes

Deposited: 2009-11-01 Released: 2009-12-01
Deposition Author(s): Jiang, L.-G., Yu, H.Y., Yuan, C., Wang, J.D., Chen, L.Q., Meehan, E.J., Huang, Z.-X., Huang, M.-D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.71 Å
R-Value Free: 0.275
R-Value Work: 0.223
R-Value Observed: 0.223

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Crystal Structures of 2-Aminobenzothiazole-based Inhibitors in Complexes with Urokinase-type Plasminogen Activator

Jiang, L.-G., Yu, H.-Y., Yuan, C., Wang, J.-D., Chen, L.-Q., Meehan, E.J., Huang, Z.-X., Huang, M.-D.

(2009) Chin J Struct Chem 28: 1427-1432

Macromolecule Content

Total Structure Weight: 28.66 kDa
Atom Count: 2,043
Modelled Residue Count: 238
Deposited Residue Count: 253
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Urokinase-type plasminogen activator	A [auth U]	253	Homo sapiens	Mutation(s): 2 Gene Names: PLAU EC: 3.4.21.73
UniProt & NIH Common Fund Data Resources
Find proteins for P00749 (Homo sapiens) Explore P00749 Go to UniProtKB: P00749
PHAROS: P00749 GTEx: ENSG00000122861
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00749
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
2BS Query on 2BS Download Ideal Coordinates CCD File SDF format, chain B [auth U] MOL2 format, chain B [auth U]	B [auth U]	ethyl 2-amino-1,3-benzothiazole-6-carboxylate C₁₀ H₁₀ N₂ O₂ S VYJSGJXWKSDUSG-UHFFFAOYSA-N		Interactions Focus chain B [auth U] Interactions & Density Focus chain B [auth U]

Binding Affinity Annotations
ID	Source	Binding Affinity
2BS	PDBBind: 3KID	Ki: 6.56e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.71 Å
R-Value Free: 0.275
R-Value Work: 0.223
R-Value Observed: 0.223
Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.216	α = 90
b = 121.216	β = 90
c = 43.299	γ = 120

Software Package:

Software Name	Purpose
PROTEUM PLUS	data collection
CNS	refinement
PROTEUM PLUS	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-12-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-12-01
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2019-12-25
Changes: Data collection
Version 1.3: 2021-11-10
Changes: Database references, Derived calculations
Version 1.4: 2023-11-01
Changes: Data collection, Refinement description

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.