4H42

Synthesis of a Weak Basic uPA Inhibitor and Crystal Structure of Complex with uPA

PDB DOI: https://doi.org/10.2210/pdb4H42/pdb

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

Deposited: 2012-09-14 Released: 2013-10-30
Deposition Author(s): Yu, H.-Y., Gao, D., Zhang, X., Jiang, L.-G., Hong, Z.-B., Yuan, C., Fang, X., Wang, J.-D., Huang, M.-D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.01 Å
R-Value Free: 0.285
R-Value Work: 0.207
R-Value Observed: 0.211

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Synthesis of a Weak Basic uPA Inhibitor and Crystal Structure of Complex with uPA

Yu, H.-Y., Gao, D., Xu, Z., Jiang, L.-G., Hong, Z.-B., Fan, X., Yuan, C., Wang, J.-D., Huang, M.

(2013) Chin J Struct Chem 32: 961-968

Macromolecule Content

Total Structure Weight: 28.49 kDa
Atom Count: 2,111
Modelled Residue Count: 248
Deposited Residue Count: 248
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]	248	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG6 Query on PG6 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-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE C₁₂ H₂₆ O₆ DMDPGPKXQDIQQG-UHFFFAOYSA-N		Interactions Focus chain C [auth U] Interactions & Density Focus chain C [auth U]
11E Query on 11E 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]	N-[(2-amino-1,3-benzothiazol-6-yl)carbonyl]glycine C₁₀ H₉ N₃ O₃ S JTXHRLUPQXMVPR-UHFFFAOYSA-N		Interactions Focus chain B [auth U] Interactions & Density Focus chain B [auth U]

Binding Affinity Annotations
ID	Source	Binding Affinity
11E	PDBBind: 4H42	Ki: 3.41e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.01 Å
R-Value Free: 0.285
R-Value Work: 0.207
R-Value Observed: 0.211
Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.916	α = 90
b = 120.916	β = 90
c = 42.875	γ = 120

Software Package:

Software Name	Purpose
PROTEUM PLUS	data collection
REFMAC	refinement

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-10-30

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-10-30
Type: Initial release
Version 1.1: 2023-12-27
Changes: Data collection, Database references, Derived calculations
Version 1.2: 2024-11-06
Changes: Structure summary

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4H42

Synthesis of a Weak Basic uPA Inhibitor and Crystal Structure of Complex with uPA

Synthesis of a Weak Basic uPA Inhibitor and Crystal Structure of Complex with uPA

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)