3MHW

The complex crystal Structure of Urokianse and 2-Aminobenzothiazole

PDB DOI: https://doi.org/10.2210/pdb3MHW/pdb

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

Deposited: 2010-04-09 Released: 2010-04-21
Deposition Author(s): Jiang, L.-G., Yuan, C., Chen, L.-Q., Huang, M.-D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.234
R-Value Work: 0.205
R-Value Observed: 0.206

Starting Model: experimental
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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: 28.09 kDa
Atom Count: 2,147
Modelled Residue Count: 246
Deposited Residue Count: 247
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]	247	Homo sapiens	Mutation(s): 1 Gene Names: Human 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ABV Query on ABV Download Ideal Coordinates CCD File SDF format, chain C [auth U] MOL2 format, chain C [auth U] mmCIF format, chain C [auth U]	C [auth U]	1,3-benzothiazol-2-amine C₇ H₆ N₂ S UHGULLIUJBCTEF-UHFFFAOYSA-N		Interactions Focus chain C [auth U] Interactions & Density Focus chain C [auth U]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain B [auth U] MOL2 format, chain B [auth U] mmCIF format, chain B [auth U]	B [auth U]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth U] Interactions & Density Focus chain B [auth U]

Binding Affinity Annotations
ID	Source	Binding Affinity
ABV	PDBBind: 3MHW	Ki: 5.03e+6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.234
R-Value Work: 0.205
R-Value Observed: 0.206
Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.276	α = 90
b = 121.276	β = 90
c = 43.136	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-04-21

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-04-21
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2021-11-10
Changes: Database references, Derived calculations
Version 1.3: 2023-11-01
Changes: Data collection, Refinement description
Version 1.4: 2024-10-30
Changes: Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.