8W3D: Fibroblast growth factor receptor 2

TAS-120 covalent structure with FGFR2 molecular brake mutant. Determined by X-ray diffraction at 2.04 Å resolution. Released 1 Jan 2025.

Method: X-ray diffraction
Resolution: 2.04 Å
Organism: Homo sapiens
Chains: 4
Atoms: 10,120
Mol. weight: 151.47 kDa
Ligands: TZ0
Released: 1 Jan 2025

Explore 8W3D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8W3D contains 78 α-helices and 56 β-strands across 4 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: 20 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	475	1	1
α-helix	478-480	3
β-strand	481-488	8	1
β-strand	494-501	8	1
β-strand	511-518	8	1
β-strand	524	1	2
α-helix	525-541	17
β-strand	547	1	3
α-helix	548-549	2
β-strand	550-554	5	1
β-strand	561-565	5	1
β-strand	571	1	3
α-helix	572-577	6
α-helix	581	1
α-helix	590-592	3
α-helix	594-599	6
α-helix	600-619	20
β-strand	622-623	2	4
α-helix	629-631	3
β-strand	632-634	3	3
β-strand	640-642	3	3
β-strand	649-650	2	4
α-helix	655	1
β-strand	656-657	2	5
β-strand	666	1	6
α-helix	667-669	3
α-helix	672-676	5
β-strand	679-680	2	5
α-helix	682-697	16
α-helix	701-702	2
α-helix	709-717	9
α-helix	722-725	4
α-helix	730-739	10
α-helix	744-746	3
α-helix	748-749	2
α-helix	750-763	14

Chain B: 19 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	475	1	7
α-helix	478-480	3
β-strand	481-488	8	7
β-strand	494-501	8	7
α-helix	510	1
β-strand	511-518	8	7
β-strand	524	1	6
α-helix	525-541	17
β-strand	547	1	8
α-helix	548-549	2
β-strand	550-554	5	7
β-strand	561-565	5	7
β-strand	571	1	8
α-helix	572-578	7
α-helix	594-596	3
α-helix	597-599	3
α-helix	600-619	20
β-strand	622-623	2	9
α-helix	629-631	3
β-strand	632-634	3	8
β-strand	640-642	3	8
β-strand	649-650	2	9
β-strand	666	1	2
α-helix	667-669	3
α-helix	672-676	5
α-helix	682-697	16
α-helix	701-702	2
α-helix	709-717	9
α-helix	722-725	4
α-helix	730-739	10
α-helix	744-746	3
α-helix	748-749	2
α-helix	750-763	14

Chain C: 20 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	475	1	10
α-helix	478-480	3
β-strand	481-488	8	10
β-strand	495-501	7	10
β-strand	511-517	7	10
α-helix	525-541	17
β-strand	547	1	11
α-helix	548-549	2
β-strand	550-554	5	10
β-strand	561-565	5	10
β-strand	571	1	11
α-helix	572-577	6
α-helix	581	1
α-helix	590-592	3
α-helix	594-599	6
α-helix	600-619	20
β-strand	622-623	2	12
α-helix	629-631	3
β-strand	632-634	3	11
β-strand	640-642	3	11
β-strand	649-650	2	12
α-helix	655	1
β-strand	656-657	2	13
α-helix	667-669	3
α-helix	672-676	5
β-strand	679-680	2	13
α-helix	682-697	16
α-helix	701-702	2
α-helix	709-717	9
α-helix	722-725	4
α-helix	730-739	10
α-helix	744-746	3
α-helix	748-749	2
α-helix	750-765	16

Chain D: 19 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	475	1	14
α-helix	478-480	3
β-strand	481-488	8	14
β-strand	495-501	7	14
β-strand	511-517	7	14
α-helix	525-541	17
β-strand	547	1	15
α-helix	548-549	2
β-strand	550-554	5	14
β-strand	561-565	5	14
β-strand	571	1	15
α-helix	572-578	7
α-helix	594-596	3
α-helix	597-599	3
α-helix	600-619	20
β-strand	622-623	2	16
α-helix	629-631	3
β-strand	632-634	3	15
β-strand	640-642	3	15
β-strand	649-650	2	16
α-helix	656-658	3
α-helix	667-669	3
α-helix	672-676	5
α-helix	682-697	16
α-helix	701-702	2
α-helix	709-717	9
α-helix	722-725	4
α-helix	730-739	10
α-helix	744-746	3
α-helix	748-749	2
α-helix	750-764	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Fibroblast growth factor receptor 2	A, B, C, D	protein	324	Homo sapiens	P21802 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>8W3D_1 Fibroblast growth factor receptor 2 (chains A, B, C, D)
MGSSHHHHHHSQDPMLAGVSEYELPEDPKWEFPRDKLTLGKPLGEGCFGQVVMAEAVGID
KDKPKEAVTVAVKMLKDDATEKDLSDLVSEMEMMKMIGKHKNIIKLLGACTQDGPLYVIV
EYASKGNLREYLRARRPPGMEYSYDINRVPEEQMTFKDLVSCTYQLARGMEYLASQKCIH
RDLAARNVLVTENNVMKIADFGLARVINNIDYYKKTTNGRLPVKWMAPEALFDRVYTHQS
DVWSFGVLMWEIFTLGGSPYPGIPVEELFKLLKEGHRMDKPANCTNELYMMMRDCWHAVP
SQRPTFKQLVEDLDRILTLTTNEE

Ligands and cofactors

ID	Name	Formula	Copies
TZ0	1-[(3S)-3-{4-amino-3-[(3,5-dimethoxyphenyl)ethynyl]-1H-pyrazolo[3,4-d]pyrimidin…	C22 H22 N6 O3	4

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

Primary citation

A model for decoding resistance in precision oncology: acquired resistance to FGFR inhibitors in cholangiocarcinoma. Goyal, L., DiToro, D., Facchinetti, F. et al. Ann Oncol (2025) 36:426-443. DOI 10.1016/j.annonc.2024.12.011 · PubMed

Other PDB entries of the same protein (UniProt P21802 (AlphaFold model), which also has an AlphaFold model), best resolution first:

10OU 1.77 Å, FGFR2 mutant D650V with compound 12
2PVF 1.8 Å, Crystal Structure of Tyrosine Phosphorylated Activated FGF Receptor 2 (FGFR2) Kinase…
3B2T 1.8 Å, Structure of phosphotransferase
4J99 1.85 Å, Crystal Structure of FGF Receptor 2 (FGFR2) Kinase Domain Harboring the Gain-of-Function…
10OO 1.85 Å, FGFR2 mutant D650V with compound 4 (AZD3463)
5UGL 1.86 Å, Crystal Structure of FGF Receptor 2 Tyrosine Kinase Domain Harboring the D650V…
3CAF 1.96 Å, Crystal Structure of hFGFR2 D2 Domain
10OQ 1.98 Å, FGFR2 mutant D650V with compound 6
9U7S 1.99 Å, FGFR2 kinase domain with a macrocyclic compound 8r
3CLY 2.0 Å, Crystal Structure of FGF Receptor 2 (FGFR2) Kinase Domains Trapped in…
5UI0 2.05 Å, Crystal Structure of the Tyrosine Kinase Domain of FGF Receptor 2 harboring an…
3OJM 2.1 Å, Crystal Structure of FGF1 complexed with the ectodomain of FGFR2b harboring P253R Apert…

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