8H75 | pdb_00008h75

FGFR2 in complex with YJ001

PDB DOI: https://doi.org/10.2210/pdb8H75/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-10-19 Released: 2023-10-25
Deposition Author(s): Yan, X.E., Yun, C.H.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.75 Å
R-Value Free:
0.238 (Depositor), 0.235 (DCC)
R-Value Work:
0.214 (Depositor), 0.226 (DCC)
R-Value Observed:
0.216 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

FGFR2 in complex with YJ001

Yan, X.E., Yun, C.H.

To be published.

Macromolecule Content

Total Structure Weight: 144.81 kDa
Atom Count: 8,793
Modeled Residue Count: 1,120
Deposited Residue Count: 1,248
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fibroblast growth factor receptor 2	A, B, C, D	312	Homo sapiens	Mutation(s): 0 Gene Names: FGFR2, BEK, KGFR, KSAM EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P21802 (Homo sapiens) Explore P21802 Go to UniProtKB: P21802
PHAROS: P21802 GTEx: ENSG00000066468
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P21802
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
KX0 (Subject of Investigation/LOI) Query on KX0 Download:Ideal Coordinates CCD File SDF format, chain I [auth D] SDF format, chain H [auth C] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain I [auth D] MOL2 format, chain H [auth C] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain I [auth D] mmCIF format, chain H [auth C] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B], H [auth C], I [auth D]	Tinengotinib C₂₀ H₁₉ Cl N₆ O DQFCVOOFMXEPOC-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth C] Focus chain I [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth C] Focus chain I [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR Query on PTR	A, B, C, D	L-PEPTIDE LINKING	C₉ H₁₂ N O₆ P		TYR

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.75 Å
R-Value Free: 0.238 (Depositor), 0.235 (DCC)
R-Value Work: 0.214 (Depositor), 0.226 (DCC)
R-Value Observed: 0.216 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.022	α = 90
b = 198.595	β = 92.94
c = 67.203	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
HKL-2000	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: 2023-10-25

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2023-10-25
Type: Initial release
Version 1.1: 2023-11-08
Changes: Derived calculations, Structure summary
Version 1.2: 2023-11-15
Changes: Data collection
Version 1.3: 2024-11-06
Changes: Structure summary

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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.