4IBM: Insulin receptor kinase domain

Crystal structure of insulin receptor kinase domain in complex with an inhibitor Irfin-1. Determined by X-ray diffraction at 1.8 Å resolution. Released 21 Aug 2013.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,330
Mol. weight: 70.27 kDa
Ligands: IR1
Released: 21 Aug 2013

Explore 4IBM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4IBM contains 43 α-helices and 26 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: 22 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	990	1	1
α-helix	993-995	3
β-strand	996-1005	10	1
β-strand	1008-1016	9	1
β-strand	1024-1031	8	1
α-helix	1038-1048	11
α-helix	1049-1051	3
β-strand	1059	1	2
α-helix	1060-1061	2
β-strand	1062-1066	5	1
β-strand	1073-1077	5	1
β-strand	1083	1	2
α-helix	1084-1090	7
α-helix	1101-1102	2
α-helix	1104-1105	2
α-helix	1106-1125	20
α-helix	1135-1137	3
β-strand	1138-1140	3	2
β-strand	1146-1148	3	2
α-helix	1159-1161	3
β-strand	1163-1165	3	3
β-strand	1169-1171	3	3
α-helix	1173-1175	3
α-helix	1178-1183	6
β-strand	1186	1	4
α-helix	1188-1204	17
α-helix	1207-1208	2
α-helix	1215-1223	9
α-helix	1228-1231	4
α-helix	1236-1245	10
α-helix	1250-1252	3
α-helix	1254-1255	2
α-helix	1256-1263	8
α-helix	1264-1266	3
α-helix	1271-1274	4

Chain B: 21 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	990	1	5
α-helix	993-995	3
β-strand	996-1004	9	5
β-strand	1009-1016	8	5
β-strand	1024-1031	8	5
α-helix	1038-1051	14
β-strand	1059	1	6
α-helix	1060-1061	2
β-strand	1062-1066	5	5
β-strand	1073-1077	5	5
β-strand	1083	1	6
α-helix	1084-1090	7
α-helix	1104-1105	2
α-helix	1106-1125	20
α-helix	1135-1137	3
β-strand	1138-1140	3	6
β-strand	1146-1148	3	6
α-helix	1159-1161	3
β-strand	1163-1164	2	7
α-helix	1166-1168	3
β-strand	1170-1171	2	7
α-helix	1173-1175	3
α-helix	1178-1183	6
β-strand	1185	1	4
α-helix	1188-1204	17
α-helix	1207-1208	2
α-helix	1215-1223	9
α-helix	1228-1231	4
α-helix	1236-1245	10
α-helix	1250-1252	3
α-helix	1254-1255	2
α-helix	1256-1263	8
α-helix	1264-1266	3
α-helix	1271-1274	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Insulin receptor	A, B	protein	306	Homo sapiens	P06213 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4IBM_1 Insulin receptor (chains A, B)
VFPCSVYVPDEWEVSREKITLLRELGQGSFGMVYEGNARDIIKGEAETRVAVKTVNESAS
LRERIEFLNEASVMKGFTCHHVVRLLGVVSKGQPTLVVMELMAHGDLKSYLRSLRPEAEN
NPGRPPPTLQEMIQMAAEIADGMAYLNAKKFVHRDLAARNCMVAHDFTVKIGDFGMTRDI
YETDYYRKGGKGLLPVRWMAPESLKDGVFTTSSDMWSFGVVLWEITSLAEQPYQGLSNEQ
VLKFVMDGGYLDQPDNCPERVTDLMRMCWQFNPNMRPTFLEIVNLLKDDLHPSFPEVSFF
HSEENK

Ligands and cofactors

ID	Name	Formula	Copies
IR1	5-(2-phenylpyrazolo[1,5-a]pyridin-3-yl)-3H-pyrazolo[3,4-c]pyridazin-3-one	C18 H10 N6 O	2

Primary citation

A highly selective dual insulin receptor (IR)/insulin-like growth factor 1 receptor (IGF-1R) inhibitor derived from an extracellular signal-regulated kinase (ERK) inhibitor. Anastassiadis, T., Duong-Ly, K.C., Deacon, S.W. et al. J Biol Chem (2013) 288:28068-28077. DOI 10.1074/jbc.M113.505032 · PubMed

Other PDB entries of the same protein (UniProt P06213 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3BU3 1.65 Å, Crystal structure of the insulin receptor kinase in complex with IRS2 KRLB peptide
5HHW 1.79 Å, Crystal structure of insulin receptor kinase domain in complex with…
5U1M 1.8 Å, Structure of the IRS-1 PTB Domain Bound to the Juxtamembrane Region of the Insulin…
1IR3 1.9 Å, Phosphorylated insulin receptor tyrosine kinase in complex with peptide substrate and…
1P14 1.9 Å, Crystal structure of a catalytic-loop mutant of the insulin receptor tyrosine kinase
3BU6 1.95 Å, Crystal structure of the insulin receptor kinase in complex with IRS2 KRLB phosphopeptide
1IRK 2.1 Å, Crystal structure of the tyrosine kinase domain of the human insulin receptor
3BU5 2.1 Å, Crystal structure of the insulin receptor kinase in complex with IRS2 KRLB peptide and ATP
3EKK 2.1 Å, Insulin receptor kinase complexed with an inhibitor
8DWN 2.15 Å, Crystal structure of bis-phosphorylated insulin receptor kinase domain
3EKN 2.2 Å, Insulin receptor kinase complexed with an inhibitor
5E1S 2.26 Å, The Crystal structure of INSR Tyrosine Kinase in complex with the Inhibitor BI 885578

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