9D5E: ILK/alpha-parvin core complex

Crystal structure of the ILK/alpha-parvin core complex bound to gefitinib. Determined by X-ray diffraction at 1.5 Å resolution. Released 29 Oct 2025.

Method: X-ray diffraction
Resolution: 1.5 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,637
Mol. weight: 46.99 kDa
Ligands: B3P, IRE
Released: 29 Oct 2025

Explore 9D5E in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9D5E contains 28 α-helices and 13 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, 12 β-strands

Element	Residues	Length	Sheet
α-helix	190-192	3
β-strand	194-202	9	1
β-strand	205-212	8	1
β-strand	215-222	8	1
α-helix	229-238	10
α-helix	239-242	4
β-strand	250-251	2	2
β-strand	253-257	5	1
β-strand	266-270	5	1
β-strand	276	1	2
α-helix	277-282	6
α-helix	291-308	18
α-helix	312-314	3
β-strand	317	1	3
α-helix	318	1
α-helix	322-324	3
β-strand	325-327	3	2
β-strand	333-336	4	2
α-helix	337-339	3
β-strand	341	1	3
β-strand	350	1	4
α-helix	353-355	3
α-helix	358-361	4
α-helix	365-367	3
α-helix	370-387	18
α-helix	397-406	10
α-helix	411-414	4
α-helix	419-428	10
α-helix	433-435	3
α-helix	437-438	2
α-helix	439-448	10

Chain B: 9 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	250-255	6
α-helix	258-276	19
α-helix	277-279	3
α-helix	294-304	11
β-strand	307	1	4
α-helix	310-312	3
α-helix	320-336	17
α-helix	339-342	4
α-helix	346-350	5
α-helix	354-368	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Integrin-linked protein kinase	A	protein	271	Homo sapiens	Q13418 (AlphaFold model)
Alpha-parvin	B	protein	129	Homo sapiens	Q9NVD7 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9D5E_1 Integrin-linked protein kinase (chains A)
MNKHSGIDFKQLNFLTKLNENHSGELWKGRWQGNDIVVKVLKVRDWSTRKSRDFNEECPR
LRIFSHPNVLPVLGACQSPPAPHPTLITHWMPYGSLYNVLHEGTNFVVDQSQAVKFALDM
ARGMAFLHTLEPLIPRHALNSRSVMIDEDMTARISMADVKFSFQSPGRMYAPAWVAPEAL
QKKPEDTNRRSADMWSFAVLLWELVTREVPFADLSNMEIGMKVALEGLRPTIPPGISPHV
SKLMKICMNEDPAKRPKFDMIVPILEKMQDK

Sequence of entity 2 (B), FASTA

>9D5E_2 Alpha-parvin (chains B)
GSHMDAFDTLFDHAPDKLNVVKKTLITFVNKHLNKLNLEVTELETQFADGVYLVLLMGLL
EGYFVPLHSFFLTPDSFEQKVLNVSFAFELMQDGGLEKPKPRPEDIVNCDLKSTLRVLYN
LFTKYRNVE

Ligands and cofactors

ID	Name	Formula	Copies
B3P	2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-pr…	C11 H26 N2 O6	1
IRE	Gefitinib	C22 H24 Cl F N4 O3	2

Primary citation

Crystal structure of the ILK/alpha-parvin core complex bound to gefitinib. Fukuda, K., Qin, J. To be published.

Other PDB entries of the same protein (UniProt Q13418 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4HI8 1.2 Å, Structure of integrin-linked kinase ankyrin repeat domain in complex with PINCH1 LIM1…
4HI9 1.2 Å, 1.2 structure of integrin-linked kinase ankyrin repeat domain in complex with PINCH1…
9TP9 1.45 Å, Crystal structure of integrin-linked kinase (ILK) in complex with Alpha-Parvin and…
9D5F 1.5 Å, Crystal structure of the ILK/alpha-parvin core complex bound to bosutinib
9D5H 1.5 Å, Crystal structure of the ILK mutant (R371Q)/alpha-parvin core complex bound to gefitinib
9D5I 1.5 Å, Crystal structure of the ILK mutant (R225A)/alpha-parvin core complex bound to MgATP
9D5P 1.5 Å, Crystal structure of the ILK/alpha-parvin core complex bound to erlotinib
9TPD 1.5 Å, Crystal structure of integrin-linked kinase (ILK) in complex with alpha-parvin and a…
9D5G 1.55 Å, Crystal structure of the ILK/alpha-parvin core complex bound to 4-methyl erlotinib
3F6Q 1.6 Å, Crystal structure of integrin-linked kinase ankyrin repeat domain in complex with PINCH1…
3KMU 1.8 Å, Crystal structure of the ILK/alpha-parvin core complex (apo)
3REP 1.8 Å, Crystal structure of the ILK/alpha-parvin core complex (MnATP)

Browse structure collections

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