Macromolecule Content

Total Structure Weight: 35.36 kDa
Atom Count: 2,444
Modelled Residue Count: 299
Deposited Residue Count: 311
Unique protein chains: 1

6JPJ

Crystal structure of FGF401 in complex of FGFR4

PDB DOI: 10.2210/pdb6JPJ/pdb

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

Deposited: 2019-03-27 Released: 2019-05-15
Deposition Author(s): Zhou, Z., Chen, X., Chen, Y.
Funding Organization(s): National Natural Science Foundation of China

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.64 Å
R-Value Free: 0.243
R-Value Work: 0.195
R-Value Observed: 0.198

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Characterization of FGF401 as a reversible covalent inhibitor of fibroblast growth factor receptor 4.

Zhou, Z., Chen, X., Fu, Y., Zhang, Y., Dai, S., Li, J., Chen, L., Xu, G., Chen, Z., Chen, Y.

(2019) Chem Commun (Camb) 55: 5890-5893

PubMed: 31041948 Search on PubMed
DOI: 10.1039/c9cc02052g
Primary Citation of Related Structures:
6JPJ

PubMed Abstract:

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): 2 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
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FGF (Subject of Investigation/LOI) Query on FGF Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	N-[5-cyano-4-(2-methoxyethylamino)pyridin-2-yl]-7-methanoyl-6-[(4-methyl-2-oxidanylidene-piperazin-1-yl)methyl]-3,4-dihydro-2H-1,8-naphthyridine-1-carboxamide C₂₅ H₃₀ N₈ O₄ BHKDKKZMPODMIQ-UHFFFAOYSA-N		Ligand Interaction
SO4 (Subject of Investigation/LOI) Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A]	C [auth A], D [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Ligand Interaction

Binding Affinity Annotations
ID	Source	Binding Affinity
FGF	BindingDB: 6JPJ	IC50: min: 1.9, max: 10 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.64 Å
R-Value Free: 0.243
R-Value Work: 0.195
R-Value Observed: 0.198
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.275	α = 90
b = 60.931	β = 98.56
c = 61.154	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2019-05-15

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2019-05-15
Type: Initial release
Version 1.1: 2019-06-05
Changes: Data collection, Database references

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.