5Z1C

The crystal structure of uPA in complex with 4-Iodobenzylamine at pH7.4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.143 
  • R-Value Work: 0.118 
  • R-Value Observed: 0.119 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Halogen bonding for the design of inhibitors by targeting the S1 pocket of serine proteases

Jiang, L.G.Zhang, X.Zhou, Y.Chen, Y.Y.Luo, Z.P.Li, J.Y.Yuan, C.Huang, M.D.

(2018) RSC Adv 49: 28189-28197


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Urokinase-type plasminogen activatorA [auth U]245Homo sapiensMutation(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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZXI (Subject of Investigation/LOI)
Query on ZXI

Download Ideal Coordinates CCD File 
B [auth U]1-(4-iodophenyl)methanamine
C7 H8 I N
KCGZGJOBKAXVSU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.143 
  • R-Value Work: 0.118 
  • R-Value Observed: 0.119 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.503α = 90
b = 120.503β = 90
c = 42.719γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31400637
National Natural Science Foundation of ChinaChina31170707
National Natural Science Foundation of ChinaChina31370737

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-26
    Type: Initial release