Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 31.86 kDa 
• Atom Count: 2433 
• Modelled Residue Count: 254 
• Deposited Residue Count: 276 
• Unique protein chains: 2

1GJB

ENGINEERING INHIBITORS HIGHLY SELECTIVE FOR THE S1 SITES OF SER190 TRYPSIN-LIKE SERINE PROTEASE DRUG TARGETS

• DOI: 10.2210/pdb1GJB/pdb

• Classification: BLOOD CLOTTING, hydrolase
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2001-04-27 Released: 2002-04-27 
• Deposition Author(s): Katz, B.A., Sprengeler, P.A., Luong, C., Verner, E., Spencer, J.R., Breitenbucher, J.G., Hui, H., McGee, D., Allen, D., Martelli, A., Mackman, R.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.259 
• R-Value Work: 0.204 
• R-Value Observed: 0.209 

Literature

Engineering inhibitors highly selective for the S1 sites of Ser190 trypsin-like serine protease drug targets.

Katz, B.A., Sprengeler, P.A., Luong, C., Verner, E., Elrod, K., Kirtley, M., Janc, J., Spencer, J.R., Breitenbucher, J.G., Hui, H., McGee, D., Allen, D., Martelli, A., Mackman, R.L.

(2001) Chem Biol 8: 1107-1121

• PubMed: 11731301 
• DOI: 10.1016/s1074-5521(01)00084-9
• Primary Citation of Related Structures:  
  1GJD, 1GJ9, 1GJ8, 1GJ7, 1GJ6, 1GJ5, 1GJ4, 1GJC, 1GJB, 1GJA


• PubMed Abstract: 
  

Involved or implicated in a wide spectrum of diseases, trypsin-like serine proteases comprise well studied drug targets and anti-targets that can be subdivided into two major classes. In one class there is a serine at position 190 at the S1 site, as in urokinase type plasminogen activator (urokinase or uPA) and factor VIIa, and in the other there is an alanine at 190, as in tissue type plasminogen activator (tPA) and factor Xa. A hydrogen bond unique to Ser190 protease-arylamidine complexes between O gamma(Ser190) and the inhibitor amidine confers an intrinsic preference for such inhibitors toward Ser190 proteases over Ala190 counterparts.

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Organizational Affiliation: 

Axys Pharmaceutical Corporation, 385 Oyster Point Boulevard, South San Francisco, CA 94080, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UROKINASE-TYPE PLASMINOGEN ACTIVATOR	A	23	Homo sapiens	Mutation(s): 0  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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
UROKINASE-TYPE PLASMINOGEN ACTIVATOR	B	253	Homo sapiens	Mutation(s): 0  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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
130	E [auth B]	2-(2-HYDROXY-BIPHENYL)-1H-BENZOIMIDAZOLE-5-CARBOXAMIDINE C20 H16 N4 O LMGQGPVCSYOMNS-UHFFFAOYSA-N
CIT	C [auth B], D [auth B]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
130	Ki:  450   nM  Binding MOAD
130	Ki :  450   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.259 
• R-Value Work: 0.204 
• R-Value Observed: 0.209 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82	α = 90
b = 49.6	β = 114.03
c = 67.3	γ = 90

Software Package:

Software Name	Purpose
bioteX	data collection
bioteX	data reduction
X-PLOR	refinement
bioteX	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-04-27 
• Released Date: 2002-04-27 
Deposition Author(s): Katz, B.A., Sprengeler, P.A., Luong, C., Verner, E., Spencer, J.R., Breitenbucher, J.G., Hui, H., McGee, D., Allen, D., Martelli, A., Mackman, R.L.

Revision History  

• Version 1.0: 2002-04-27
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Atomic model, Version format compliance
• Version 1.3: 2017-10-04
  Changes: Advisory, Refinement description