3IG6

Low molecular weigth human Urokinase type Plasminogen activator 2-[6-(3'-Aminomethyl-biphenyl-3-yloxy)-4-(3-dimethylamino-pyrrolidin-1-yl)-3,5-difluoro-pyridin-2-yloxy]-4-dimethylamino-benzoic acid complex

Structural Biology Knowledgebase: 3IG6 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.228
  • R-Value Work: 0.197

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3IG6

Classification: HYDROLASE

Total Structure Weight: 63639.92

Macromolecule Entities
Molecule Chains Length Organism Details
Urokinase-type plasminogen activator A, C 23 Homo sapiens EC#: 3.4.21.73 IUBMB
Fragment: FRAGMENT OF LIGHT CHAIN
Gene Name(s): PLAU Gene View
Urokinase-type plasminogen activator B, D 253 Homo sapiens EC#: 3.4.21.73 IUBMB
Fragment: CATALYTIC DOMAIN
Gene Name(s): PLAU Gene View

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
438
Query on 438

B, D 2-[(6-{[3'-(aminomethyl)biphenyl-3-yl]oxy}- 4-[(3R)-3-(dimethylamino)pyrrolidin-1-yl]- 3,5-difluoropyridin-2-yl)oxy]-4-(dimethylamino)benzoic acid
C33 H35 F2 N5 O4
WIFBOPRNBMRLLS-XMMPIXPASA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

D PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
438 N/A in BindingDB
IC50: 25 nM  BindingMOAD
IC50: 25 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.228
  • R-Value Work: 0.197
  • Space Group: P 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 70.86 α = 90.00
b = 52.29 β = 90.23
c = 72.58 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-07-27
  • Released Date: 2009-10-13
  • Deposition author(s): Adler, M., Whitlow, M.

Revision History

  • 2011-11-16
    Type: Atom occupancy | Details: Atom occupancy
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4