6YVS: FOCAL ADHESION KINASE CATALYTIC DOMAIN

FOCAL ADHESION KINASE CATALYTIC DOMAIN IN COMPLEX WITH 5-{4-[(Pyridin-3-ylmethyl)-amino]-5-trifluoromethyl-pyrimidin-2-ylamino}-1,3-dihydro-indol-2-one. Determined by X-ray diffraction at 1.81 Å resolution. Released 10 Feb 2021.

Method: X-ray diffraction
Resolution: 1.81 Å
Organism: Homo sapiens
Chains: 4
Atoms: 9,136
Mol. weight: 130.91 kDa
Ligands: PVT
Released: 10 Feb 2021

Explore 6YVS in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6YVS contains 75 α-helices and 40 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: 17 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	416	1	1
α-helix	419-421	3
β-strand	422-430	9	1
β-strand	435-441	7	1
β-strand	449-455	7	1
α-helix	462-475	14
β-strand	483	1	2
α-helix	484-485	2
β-strand	486-490	5	1
α-helix	495	1
β-strand	496-500	5	1
β-strand	505-506	2	2
α-helix	507-513	7
α-helix	520-539	20
α-helix	549-551	3
β-strand	552-556	5	2
β-strand	559-562	4	2
α-helix	586-588	3
α-helix	591-596	6
α-helix	601-616	16
α-helix	620-621	2
α-helix	628-636	9
α-helix	641-644	4
α-helix	649-658	10
α-helix	663-665	3
α-helix	667-668	2
α-helix	669-684	16

Chain B: 19 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	416	1	3
α-helix	419-421	3
β-strand	422-430	9	3
β-strand	435-441	7	3
β-strand	449-455	7	3
α-helix	462-476	15
β-strand	483	1	4
α-helix	484-485	2
β-strand	486-490	5	3
α-helix	495	1
β-strand	496-500	5	3
β-strand	505-506	2	4
α-helix	507-514	8
α-helix	515-517	3
α-helix	520-539	20
α-helix	549-551	3
β-strand	552-556	5	4
β-strand	559-562	4	4
α-helix	586-588	3
α-helix	591-596	6
α-helix	601-616	16
α-helix	620-621	2
α-helix	628-630	3
α-helix	631-636	6
α-helix	641-644	4
α-helix	649-658	10
α-helix	663-665	3
α-helix	667-668	2
α-helix	669-684	16

Chain C: 18 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	416	1	5
α-helix	419-421	3
β-strand	422-430	9	5
β-strand	435-441	7	5
β-strand	449-455	7	5
α-helix	462-476	15
β-strand	483	1	6
α-helix	484-485	2
β-strand	486-490	5	5
α-helix	495	1
β-strand	496-500	5	5
β-strand	505-506	2	6
α-helix	507-513	7
α-helix	520-539	20
α-helix	549-551	3
β-strand	552-556	5	6
β-strand	559-562	4	6
α-helix	586-588	3
α-helix	591-596	6
α-helix	601-616	16
α-helix	620-621	2
α-helix	628-630	3
α-helix	631-636	6
α-helix	641-644	4
α-helix	649-658	10
α-helix	663-665	3
α-helix	667-668	2
α-helix	669-684	16

Chain D: 21 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	413-415	3
β-strand	416	1	1
α-helix	419-421	3
β-strand	422-430	9	1
β-strand	435-441	7	1
α-helix	447-448	2
β-strand	449-455	7	1
α-helix	462-476	15
β-strand	483	1	7
α-helix	484-485	2
β-strand	486-490	5	1
α-helix	495	1
β-strand	496-500	5	1
β-strand	505-506	2	7
α-helix	507-514	8
α-helix	515-517	3
α-helix	520-539	20
α-helix	549-551	3
β-strand	552-556	5	7
β-strand	559-562	4	7
α-helix	586-588	3
α-helix	591-596	6
α-helix	601-616	16
α-helix	620-621	2
α-helix	628-630	3
α-helix	631-636	6
α-helix	641-644	4
α-helix	649-658	10
α-helix	663-665	3
α-helix	667-668	2
α-helix	669-684	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Focal adhesion kinase 1	A, B, C, D	protein	282	Homo sapiens	Q05397 (AlphaFold model)

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

>6YVS_1 Focal adhesion kinase 1 (chains A, B, C, D)
GSGSTRDYEIQRERIELGRCIGEGQFGDVHQGIYMSPENPALAVAIKTCKNCTSDSVREK
FLQEALTMRQFDHPHIVKLIGVITENPVWIIMELCTLGELRSFLQVRKYSLDLASLILYA
YQLSTALAYLESKRFVHRDIAARNVLVSSNDCVKLGDFGLSRYMEDSTYYKASKGKLPIK
WMAPESINFRRFTSASDVWMFGVCMWEILMHGVKPFQGVKNNDVIGRIENGERLPMPPNC
PPTLYSLMTKCWAYDPSRRPRFTELKAQLSTILEEEKAQQEE

Ligands and cofactors

ID	Name	Formula	Copies
PVT	5-[[4-(pyridin-3-ylmethylamino)-5-(trifluoromethyl)pyrimidin-2-yl]amino]-1,3-di…	C19 H15 F3 N6 O	4

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

Primary citation

Structure-kinetic relationship reveals the mechanism of selectivity of FAK inhibitors over PYK2. Berger, B.T., Amaral, M., Kokh, D.B. et al. Cell Chem Biol (2021) 28:686. DOI 10.1016/j.chembiol.2021.01.003 · PubMed

Other PDB entries of the same protein (UniProt Q05397 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6YOJ 1.36 Å, FOCAL ADHESION KINASE CATALYTIC DOMAIN IN COMPLEX WITH 6-[4-(3-Methanesulfonyl-benzylamin…
6YT6 1.54 Å, FOCAL ADHESION KINASE CATALYTIC DOMAIN IN COMPLEX WITH N-Methyl-N-(3-{[2-(2-oxo-2,3-dihyd…
4I4E 1.55 Å, Structure of Focal Adhesion Kinase catalytic domain in complex with hinge binding…
1MP8 1.6 Å, Crystal structure of Focal Adhesion Kinase (FAK)
4EBV 1.67 Å, Structure of Focal Adhesion Kinase catalytic domain in complex with novel allosteric…
4I4F 1.75 Å, Structure of Focal Adhesion Kinase catalytic domain in complex with an allosteric…
6YQ1 1.78 Å, FOCAL ADHESION KINASE CATALYTIC DOMAIN IN COMPLEX WITH N-Methyl-N-(3-{[2-(2-oxo-1,2,3,4-t…
3PXK 1.79 Å, FOCAL ADHESION KINASE CATALYTIC DOMAIN IN COMPLEX WITH Pyrrolo[2,3-d]thiazole
6YVY 1.92 Å, FOCAL ADHESION KINASE CATALYTIC DOMAIN IN COMPLEX WITH 4-{[4-{[(1R,2R)-2-(dimethylamino)c…
6YR9 1.93 Å, FOCAL ADHESION KINASE CATALYTIC DOMAIN IN COMPLEX WITH N-Methyl-N-(2-{[2-(2-oxo-2,3-dihyd…
7W8I 1.94 Å, Crystal structure of Zn bound human Focal Adhesion Targeting (FAT) domain of the Focal…
1K04 1.95 Å, Crystal Structure of the Focal Adhesion Targeting Domain of Focal Adhesion Kinase

Browse structure collections

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