4WV1

Crystal structure of the FGFR2 D2 domain in complex with Fab 2B.1.3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.362 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Redesigning a Monospecific Anti-FGFR3 Antibody to Add Selectivity for FGFR2 and Expand Antitumor Activity.

Yin, Y.Djakovic, S.Marsters, S.Tien, J.Peng, J.Tremayne, J.Lee, G.Neve, R.M.Wu, Y.Merchant, M.Ashkenazi, A.Carter, P.J.

(2015) Mol.Cancer Ther. 14: 2270-2278

  • DOI: 10.1158/1535-7163.MCT-14-1050

  • PubMed Abstract: 
  • FGF receptors (FGFR) are attractive candidate targets for cancer therapy because they are dysregulated in several human malignancies. FGFR2 and FGFR3 can be inhibited potentially without disrupting adult tissue homeostasis. In contrast, blocking the ...

    FGF receptors (FGFR) are attractive candidate targets for cancer therapy because they are dysregulated in several human malignancies. FGFR2 and FGFR3 can be inhibited potentially without disrupting adult tissue homeostasis. In contrast, blocking the closely related FGFR1 and FGFR4, which regulate specific metabolic functions, carries a greater safety risk. An anti-FGFR3 antibody was redesigned here to create function-blocking antibodies that bind with dual specificity to FGFR3 and FGFR2 but spare FGFR1 and FGFR4. R3Mab, a previously developed monospecific anti-FGFR3 antibody, was modified via structure-guided phage display and acquired additional binding to FGFR2. The initial variant was trispecific, binding tightly to FGFR3 and FGFR2 and moderately to FGFR4, while sparing FGFR1. The X-ray crystallographic structure indicated that the antibody variant was bound to a similar epitope on FGFR2 as R3Mab on FGFR3. The antibody was further engineered to decrease FGFR4-binding affinity while retaining affinity for FGFR3 and FGFR2. The resulting dual-specific antibodies blocked FGF binding to FGFR3 and FGFR2 and inhibited downstream signaling. Moreover, they displayed efficacy in mice against human tumor xenografts overexpressing FGFR3 or FGFR2. Thus, a monospecific antibody can be exquisitely tailored to confer or remove binding to closely related targets to expand and refine therapeutic potential.


    Organizational Affiliation

    Department of Antibody Engineering, Genentech, Inc., South San Francisco, California.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fibroblast growth factor receptor 2
F, C
99Homo sapiensMutation(s): 0 
Gene Names: FGFR2 (BEK, KGFR, KSAM)
EC: 2.7.10.1
Find proteins for P21802 (Homo sapiens)
Go to Gene View: FGFR2
Go to UniProtKB:  P21802
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Fab heavy chain
B, E
230N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Fab light chain
A, D
214N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.362 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.198 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 76.087α = 90.00
b = 181.239β = 113.72
c = 94.427γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-11-04 
  • Released Date: 2015-09-16 
  • Deposition Author(s): Yin, Y., Carter, P.J.

Revision History 

  • Version 1.0: 2015-09-16
    Type: Initial release
  • Version 1.1: 2015-09-23
    Type: Derived calculations
  • Version 1.2: 2015-10-14
    Type: Database references