2WD1

Human c-Met Kinase in complex with azaindole inhibitor

• PDB DOI: https://doi.org/10.2210/pdb2WD1/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2009-03-19 Released: 2009-04-28 
• Deposition Author(s): Porter, J., Lumb, S., Franklin, R.J., Gascon-Simorte, J.M., Calmiano, M., Le Riche, K., Lallemand, B., Keyaerts, J., Edwards, H., Maloney, A., Delgado, J., King, L., Foley, A., Lecomte, F., Reuberson, J., Meier, C., Batchelor, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.265 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

Literature

Discovery of 4-Azaindoles as Novel Inhibitors of C- met Kinase.

Porter, J., Lumb, S., Franklin, R.J., Gascon-Simorte, J.M., Calmiano, M., Riche, K.L., Lallemand, B., Keyaerts, J., Edwards, H., Maloney, A., Delgado, J., King, L., Foley, A., Lecomte, F., Reuberson, J., Meier, C., Batchelor, M.

(2009) Bioorg Med Chem Lett 19: 2780

• PubMed: 19369077 
• DOI: https://doi.org/10.1016/j.bmcl.2009.03.110
• Primary Citation of Related Structures:  
  2WD1


• PubMed Abstract: 
  

  A series of 4-azaindole inhibitors of c-Met kinase is described. The postulated binding mode was confirmed by an X-ray crystal structure and series optimisation was performed on the basis of this structure. Future directions for series development are discussed.

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Organizational Affiliation: 

UCB Celltech, Slough, United Kingdom. [e-mail]

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 33.57 kDa 
• Atom Count: 2,438 
• Modelled Residue Count: 289 
• Deposited Residue Count: 292 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HEPATOCYTE GROWTH FACTOR RECEPTOR	A	292	Homo sapiens	Mutation(s): 0  EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P08581 (Homo sapiens) Explore P08581  Go to UniProtKB:  P08581
PHAROS:  P08581 GTEx:  ENSG00000105976

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZZY	B [auth A]	1-[(2-NITROPHENYL)SULFONYL]-1H-PYRROLO[3,2-B]PYRIDINE-6-CARBOXAMIDE C14 H10 N4 O5 S USLOIFPDNUDIEG-UHFFFAOYSA-N
GBL	C [auth A], D [auth A]	GAMMA-BUTYROLACTONE C4 H6 O2 YEJRWHAVMIAJKC-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
ZZY	BindingDB:  2WD1	IC50: 82 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.265 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.411	α = 90
b = 42.312	β = 93.01
c = 84.826	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-04-28 
Deposition Author(s): Porter, J., Lumb, S., Franklin, R.J., Gascon-Simorte, J.M., Calmiano, M., Le Riche, K., Lallemand, B., Keyaerts, J., Edwards, H., Maloney, A., Delgado, J., King, L., Foley, A., Lecomte, F., Reuberson, J., Meier, C., Batchelor, M.

Revision History  

• Version 1.0: 2009-04-28
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other