9WFK: FGFR1 kinase domain

Crystal structure of FGFR1 kinase domain in complex with LJ5368((2R,3R,4S,5R)-2-(4-amino-5-(7-methoxy-5-methylbenzo[b]thiophen-2-yl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)-5-(hydroxymethyl)tetrahydrofuran-3,4-diol). Determined by X-ray diffraction at 1.89 Å resolution. Released 26 Aug 2026.

Method: X-ray diffraction
Resolution: 1.89 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,771
Mol. weight: 71.13 kDa
Ligands: A1MBJ
Released: 26 Aug 2026

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

Secondary structure: helices and β-sheets

9WFK contains 35 α-helices and 20 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: 18 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	478-485	8	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	568	1	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	663-666	4
α-helix	669-673	5
α-helix	679-694	16
α-helix	698-699	2
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	747-760	14

Chain B: 17 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	465-467	3
β-strand	472	1	3
α-helix	475-477	3
β-strand	478-486	9	3
β-strand	491-498	8	3
β-strand	508-515	8	3
α-helix	522-538	17
β-strand	544	1	4
β-strand	547-551	5	3
β-strand	558-562	5	3
β-strand	568	1	4
α-helix	569-574	6
α-helix	597-616	20
α-helix	626-628	3
β-strand	629-631	3	4
β-strand	637-639	3	4
α-helix	644-646	3
α-helix	663-666	4
α-helix	669-674	6
α-helix	679-694	16
α-helix	698-699	2
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	747-760	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fibroblast growth factor receptor 1	A, B	protein	308	Homo sapiens	P11362 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9WFK_1 Fibroblast growth factor receptor 1 (chains A, B)
AGVSEYELPEDPRWELPRDRLVLGKPLGEGAFGQVVLAEAIGLDKDKPNRVTKVAVKMLK
SDATEKDLSDLISEMEMMKMIGKHKNIINLLGACTQDGPLYVIVEYASKGNLREYLQARR
PPGLEYSYNPSHNPEEQLSSKDLVSCAYQVARGMEYLASKKCIHRDLAARNVLVTEDNVM
KIADFGLARDIHHIDYYKKTTNGRLPVKWMAPEALFDRIYTHQSDVWSFGVLLWEIFTLG
GSPYPGVPVEELFKLLKEGHRMDKPSNCTNELYMMMRDCWHAVPSQRPTFKQLVEDLDRI
VALTSNQE

Ligands and cofactors

ID	Name	Formula	Copies
A1MBJ	(2~{R},3~{R},4~{S},5~{R})-2-[4-azanyl-5-(7-methoxy-5-methyl-1-benzothiophen-2-y…	C21 H22 N4 O5 S	2

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

Primary citation

Crystal structure of FGFR1 kinase domain in complex with LJ5368((2R,3R,4S,5R)-2-(4-amino-5-(7-methoxy-5-methylbenzo[b]thiophen-2-yl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)-5-(hydroxymethyl)tetrahydrofuran-3,4-diol). Moon, S.H., Ko, H.L., Park, J.H. et al. To be published.

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
9UHI 1.76 Å, FGFR1 kinase domain with a covalent inhibitor 9o
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
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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