8JMZ: FGFR1 kinase domain with sulfatinib

FGFR1 kinase domain with sulfatinib. Determined by X-ray diffraction at 1.99 Å resolution. Released 27 Mar 2024.

Method: X-ray diffraction
Resolution: 1.99 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,278
Mol. weight: 72.54 kDa
Ligands: UKI
Released: 27 Mar 2024

Explore 8JMZ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8JMZ 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: 21 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	472	1	1
α-helix	475-477	3
β-strand	478-486	9	1
β-strand	490-498	9	1
β-strand	508-516	9	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	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: 18 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
α-helix	484	1
β-strand	488	1	4
β-strand	490	1	4
β-strand	492-498	7	3
β-strand	508-514	7	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	569-575	7
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	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	310	Homo sapiens	P11362 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8JMZ_1 Fibroblast growth factor receptor 1 (chains A, B)
GPAGVSEYELPEDPRWELPRDRLVLGKPLGEGCFGQVVLAEAIGLDKDKPNRVTKVAVKM
LKSDATEKDLSDLISEMEMMKMIGKHKNIINLLGACTQDGPLYVIVEYASKGNLREYLQA
RRPPGLEYSYNPSHNPEEQLSSKDLVSCAYQVARGMEYLASKKCIHRDLAARNVLVTEDN
VMKIADFGLARDIHHIDYYKKTTNGRLPVKWMAPEALFDRIYTHQSDVWSFGVLLWEIFT
LGGSPYPGVPVEELFKLLKEGHRMDKPSNCTNELYMMMRDCWHAVPSQRPTFKQLVEDLD
RIVALTSNQE

Ligands and cofactors

ID	Name	Formula	Copies
UKI	Sulfatinib	C24 H28 N6 O3 S	2

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

Primary citation

Structural basis and selectivity of sulfatinib binding to FGFR and CSF-1R. Lin, Q., Dai, S., Qu, L. et al. Commun Chem (2024) 7:3-3. DOI 10.1038/s42004-023-01084-0 · 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
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
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…

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