5XFF

Crystal structure of LY2874455 in complex of FGFR4 gatekeeper mutation (V550L)

PDB DOI: https://doi.org/10.2210/pdb5XFF/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2017-04-10 Released: 2018-09-05
Deposition Author(s): Wu, D., Chen, Y.
Funding Organization(s): National Natural Science Foundation of China

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.320
R-Value Work: 0.265
R-Value Observed: 0.270

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

LY2874455 potently inhibits FGFR gatekeeper mutants and overcomes mutation-based resistance.

Wu, D., Guo, M., Min, X., Dai, S., Li, M., Tan, S., Li, G., Chen, X., Ma, Y., Li, J., Jiang, L., Qu, L., Zhou, Z., Chen, Z., Chen, L., Xu, G., Chen, Y.

(2018) Chem Commun (Camb) 54: 12089-12092

PubMed: 30298149 Search on PubMed
DOI: https://doi.org/10.1039/c8cc07546h
Primary Citation of Related Structures:
5XFF, 5XFJ

PubMed Abstract:
The chemical compound LY2874455 has the potential to overcome drug resistance driven by FGFR gatekeeper mutations. X-ray crystallographic studies provide the structural explanation for why this compound is effective against the FGFR gatekeeper mutations.

Organizational Affiliation

Laboratory of Structural Biology, Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, XiangYa Hospital, Central South University, Changsha, Hunan 410008, China. yonghenc@163.com.

Macromolecule Content

Total Structure Weight: 35.15 kDa
Atom Count: 2,158
Modelled Residue Count: 269
Deposited Residue Count: 311
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fibroblast growth factor receptor 4	A	311	Homo sapiens	Mutation(s): 1 Gene Names: FGFR4, JTK2, TKF EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P22455 (Homo sapiens) Explore P22455 Go to UniProtKB: P22455
PHAROS: P22455
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P22455
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
6LF Query on 6LF Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	2-[4-[E-2-[5-[(1R)-1-[3,5-bis(chloranyl)pyridin-4-yl]ethoxy]-1H-indazol-3-yl]ethenyl]pyrazol-1-yl]ethanol C₂₁ H₁₉ Cl₂ N₅ O₂ GKJCVYLDJWTWQU-CXLRFSCWSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.320
R-Value Work: 0.265
R-Value Observed: 0.270
Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.291	α = 90
b = 62.291	β = 90
c = 184.586	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data collection
HKL-3000	data reduction
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2018-09-05

Deposition Author(s):

Wu, D.

Chen, Y.

Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	81372904
National Natural Science Foundation of China	China	81570537
National Natural Science Foundation of China	China	81272971