9UHI: FGFR1 kinase domain with a covalent inhibitor 9o

FGFR1 kinase domain with a covalent inhibitor 9o. Determined by X-ray diffraction at 1.76 Å resolution. Released 24 Sept 2025.

Method: X-ray diffraction
Resolution: 1.76 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,317
Mol. weight: 72.03 kDa
Ligands: A1EPF
Released: 24 Sept 2025

Explore 9UHI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9UHI contains 39 α-helices and 22 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 22 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	465-467	3
β-strand	472	1	1
α-helix	475-477	3
β-strand	478-486	9	1
β-strand	491-498	8	1
β-strand	508-515	8	1
α-helix	522-538	17
β-strand	544	1	2
β-strand	547-551	5	1
β-strand	558-562	5	1
β-strand	567-568	2	2
α-helix	569-574	6
α-helix	577-578	2
α-helix	593-596	4
α-helix	597-616	20
α-helix	626-628	3
β-strand	629-631	3	2
β-strand	637-639	3	2
α-helix	644-647	4
α-helix	650-651	2
α-helix	655-657	3
α-helix	663-666	4
α-helix	669-674	6
α-helix	679-694	16
α-helix	698-699	2
α-helix	706-708	3
α-helix	709-714	6
α-helix	719-722	4
α-helix	727-736	10
α-helix	741-743	3
α-helix	745-746	2
α-helix	747-760	14

Chain B: 17 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	459-462	4
α-helix	465-467	3
β-strand	472	1	3
α-helix	475-477	3
β-strand	478-483	6	3
β-strand	491-498	8	3
β-strand	501	1	4
β-strand	504	1	4
β-strand	508-515	8	3
α-helix	522-538	17
β-strand	544	1	5
β-strand	547-551	5	3
β-strand	558-562	5	3
β-strand	568	1	5
α-helix	569-574	6
α-helix	577-579	3
α-helix	597-616	20
α-helix	626-628	3
β-strand	629-631	3	5
β-strand	637-639	3	5
α-helix	663-666	4
α-helix	669-674	6
α-helix	679-694	16
α-helix	706-714	9
α-helix	719-722	4
α-helix	727-736	10
α-helix	741-743	3
α-helix	745-746	2
α-helix	747-759	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fibroblast growth factor receptor 1	A, B	protein	310	Homo sapiens	P11362 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9UHI_1 Fibroblast growth factor receptor 1 (chains A, B)
GPAGVSEYELPEDPRWELPRDRLVLGKPLGEGCFGQVVLAEAIGLDKDKPNRVTKVAVKM
LKSDATEKDLSDLISEMEMMKMIGKHKNIINLLGACTQDGPLYVIVEYASKGNLREYLQA
RRPPGLEYSYNPSHNPEEQLSSKDLVSCAYQVARGMEYLASKKCIHRDLAARNVLVTEDN
VMKIADFGLARDIHHIDYYKKTTNGRLPVKWMAPEALFDRIYTHQSDVWSFGVLLWEIFT
LGGSPYPGVPVEELFKLLKEGHRMDKPSNCTNELYMMMRDCWHAVPSQRPTFKQLVEDLD
RIVALTSNQE

Ligands and cofactors

ID	Name	Formula	Copies
A1EPF	~{N}-[1-methyl-3-[3-[1-(2-morpholin-4-ylethyl)pyrazol-4-yl]quinoxalin-5-yl]indo…	C29 H31 N7 O2	2

Water and common crystallization additives (SO4) are not listed.

Primary citation

Design, Synthesis and Biological Evaluation of 7-(1-Methyl-1 H -indole-3-yl)-5 H -pyrrolo[2,3- b ]pyrazine Derivatives as Novel Covalent pan-FGFR Inhibitors to Overcome Clinical Resistance. Deng, W., Chen, X., Yan, L. et al. J Med Chem (2025) 68:19415-19437. DOI 10.1021/acs.jmedchem.5c01594 · PubMed

Other PDB entries of the same protein (UniProt P11362 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5EW8 1.63 Å, Fibroblast growth factor receptor 1 in complex with jnj-4275693
4WUN 1.65 Å, Structure of FGFR1 in complex with AZD4547 (N-{3-[2-(3,5-DIMETHOXYPHENYL)ETHYL]-1H-PYRAZO…
9U7G 1.66 Å, FGFR1 kinase domain with a macrocyclic compound 8g
7OZB 1.71 Å, FGFR1 kinase domain (residues 458-765) with mutations C488A, C584S in complex with 38.
8XZ7 1.75 Å, FGFR1 kinase domain with a covalent inhibitor 10h
9VLJ 1.81 Å, Crystal structure of FGFR1 in complex with covalent inhibitor 10a
7OZD 1.82 Å, FGFR1 kinase domain (residues 458-765) with mutations C488A, C584S in complex with 34.
7OZF 1.82 Å, FGFR1 kinase domain (residues 458-765) with mutations C488A, C584S in complex with 19.
9UHC 1.88 Å, FGFR1 kinase domain with a covalent inhibitor 9p
9WFK 1.89 Å, Crystal structure of FGFR1 kinase domain in complex with…
9WGT 1.9 Å, Crystal structure of FGFR1 kinase domain in complex with…
5O49 1.91 Å, Human FGF in complex with a covalent inhibitor

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