5DEW: PAK1

Crystal structure of PAK1 in complex with an inhibitor compound 5. Determined by X-ray diffraction at 1.9 Å resolution. Released 21 Sept 2016.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,019
Mol. weight: 67.58 kDa
Ligands: 59N
Released: 21 Sept 2016

Explore 5DEW in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5DEW contains 38 α-helices and 23 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: 19 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	251-259	9
β-strand	263	1	1
α-helix	266-268	3
β-strand	270-279	10	1
β-strand	282-289	8	1
β-strand	295-302	8	1
α-helix	309-320	12
β-strand	327	1	2
β-strand	330-336	7	1
β-strand	339-345	7	1
β-strand	351	1	2
α-helix	352-358	7
α-helix	363-382	20
β-strand	385-386	2	3
α-helix	392-394	3
β-strand	395-397	3	2
β-strand	403-405	3	2
β-strand	412-413	2	3
β-strand	421	1	4
α-helix	428-430	3
α-helix	433-436	4
β-strand	441	1	4
α-helix	444-459	16
α-helix	469-479	11
α-helix	482-484	3
α-helix	487-489	3
α-helix	492-501	10
α-helix	510-511	2
α-helix	512-515	4
α-helix	519-523	5
α-helix	524-526	3
α-helix	527-530	4
α-helix	531-540	10

Chain B: 19 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	257-259	3
α-helix	262	1
α-helix	266-269	4
β-strand	270-277	8	5
β-strand	283-289	7	5
β-strand	295-302	8	5
α-helix	309-321	13
β-strand	327	1	6
α-helix	328-329	2
β-strand	330-336	7	5
β-strand	339-345	7	5
β-strand	351	1	6
α-helix	352-358	7
α-helix	363-382	20
α-helix	392-394	3
β-strand	395-397	3	6
β-strand	403-405	3	6
α-helix	423-424	2
α-helix	433-436	4
α-helix	444-459	16
α-helix	469-479	11
α-helix	492-501	10
α-helix	510-511	2
α-helix	512-515	4
α-helix	519-523	5
α-helix	524-526	3
α-helix	527-530	4
α-helix	531-541	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Serine/threonine-protein kinase PAK 1	A, B	protein	297	Homo sapiens	Q13153 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5DEW_1 Serine/threonine-protein kinase PAK 1 (chains A, B)
SDEEILEKLRSIVSVGDPKKKYTRFEKIGQGASGTVYTAMDVATGQEVAIKQMNLQQQPK
KELIINEILVMRENKNPNIVNYLDSYLVGDELWVVMEYLAGGSLTDVVTETCMDEGQIAA
VCRECLQALEFLHSNQVIHRNIKSDNILLGMDGSVKLTDFGFCAQITPEQSKRSEMVGTP
YWMAPEVVTRKAYGPKVDIWSLGIMAIEMIEGEPPYLNENPLRALYLIATNGTPELQNPE
KLSAIFRDFLNRCLEMDVEKRGSAKELLQHQFLKIAKPLSSLTPLIAAAKEATKNNH

Ligands and cofactors

ID	Name	Formula	Copies
59N	8-[(trans-4-aminocyclohexyl)methyl]-6-[2-chloro-4-(6-methylpyrazin-2-yl)phenyl]…	C27 H30 Cl N7 O	2

Primary citation

Design of Selective PAK1 Inhibitor G-5555: Improving Proper-ties by Employing an Unorthodox Low-pKa Polar Moiety. Ndubaku, C.O. To be published.

Other PDB entries of the same protein (UniProt Q13153 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3FXZ 1.64 Å, Crystal structure of PAK1 kinase domain with ruthenium complex lambda-FL172
2QME 1.75 Å, Crystal structure of human RAC3 in complex with CRIB domain of human p21-activated…
9N4U 1.77 Å, Crystal structure of PAK1 bound to compound R1
1YHV 1.8 Å, Crystal Structure of PAK1 kinase domain with two point mutations (K299R, T423E)
1YHW 1.8 Å, Crystal Structure of PAK1 kinase domain with one point mutations (K299R)
8X5Z 1.8 Å, The Crystal Structure of PAK1 kinase domain from Biortus.
3Q52 1.8 Å, Structure of phosphorylated PAK1 kinase domain
9D4V 1.84 Å, Structure of PAK1 in complex with compound 7
9D4X 1.85 Å, Structure of PAK1 in complex with compound 16
9D4Y 1.85 Å, Structure of PAK1 in complex with compound 31
9N48 1.85 Å, Crystal structure of PAK1 bound to compound C1
3Q4Z 1.89 Å, Structure of unphosphorylated PAK1 kinase domain

Browse structure collections

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