6C1B | pdb_00006c1b

FGFR1 kinase complex with inhibitor SN37118

PDB DOI: https://doi.org/10.2210/pdb6C1B/pdb

Classification: Transferase/Transferase inhibitor
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2018-01-04 Released: 2019-01-16
Deposition Author(s): Yosaatmadja, Y., Smaill, J.B., Squire, C.J.
Funding Organization(s): Health Research Council (HRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.255 (Depositor), 0.222 (DCC)
R-Value Work:
0.220 (Depositor)
R-Value Observed:
0.222 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Understanding the structural requirements for covalent inhibition of FGFR1-3

Yosaatmadja, Y., Squire, C.J., Patterson, A.V., Smaill, J.B.

To be published.

Macromolecule Content

Total Structure Weight: 71.96 kDa
Atom Count: 4,201
Modeled Residue Count: 521
Deposited Residue Count: 622
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fibroblast growth factor receptor 1	A, B	311	Homo sapiens	Mutation(s): 2 Gene Names: FGFR1, BFGFR, CEK, FGFBR, FLG, FLT2, HBGFR EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P11362 (Homo sapiens) Explore P11362 Go to UniProtKB: P11362
PHAROS: P11362 GTEx: ENSG00000077782
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P11362
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
YY4 (Subject of Investigation/LOI) Query on YY4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	3-(2,6-dichloro-3,5-dimethoxyphenyl)-1-{(3S)-1-[(2E)-4-(dimethylamino)but-2-enoyl]pyrrolidin-3-yl}-7-(phenylamino)-3,4-dihydropyrimido[4,5-d]pyrimidin-2(1H)-one C₃₀ H₃₃ Cl₂ N₇ O₄ PBXZRBBBLQGCRI-MAIVGLDJSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.255 (Depositor), 0.222 (DCC)
R-Value Work: 0.220 (Depositor)
R-Value Observed: 0.222 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 213.514	α = 90
b = 52.193	β = 107.03
c = 65.795	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-01-16

Deposition Author(s):

Yosaatmadja, Y.

Funding Organization	Location	Grant Number
Health Research Council (HRC)	New Zealand	--

Revision History (Full details and data files)

Version 1.0: 2019-01-16
Type: Initial release
Version 1.1: 2020-01-01
Changes: Author supporting evidence
Version 1.2: 2023-10-04
Changes: Data collection, Database references, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.