2ZM3: Insulin-like growth factor 1 receptor

Complex Structure of Insulin-like Growth Factor Receptor and Isoquinolinedione Inhibitor. Determined by X-ray diffraction at 2.5 Å resolution. Released 10 Jun 2008.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 4
Atoms: 10,157
Mol. weight: 143.07 kDa
Ligands: 575
Released: 10 Jun 2008

Explore 2ZM3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2ZM3 contains 79 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, 14 β-strands

Element	Residues	Length	Sheet
α-helix	983-985	3
β-strand	993	1	1
α-helix	996-998	3
β-strand	999-1007	9	1
β-strand	1012-1022	11	1
β-strand	1025-1035	11	1
α-helix	1041-1056	16
β-strand	1062	1	2
α-helix	1063-1064	2
β-strand	1065-1069	5	1
β-strand	1075-1080	6	1
β-strand	1086	1	2
α-helix	1087-1092	6
α-helix	1106-1108	3
α-helix	1109-1128	20
β-strand	1131-1132	2	3
α-helix	1138-1140	3
β-strand	1141-1143	3	2
β-strand	1149-1151	3	2
β-strand	1158-1159	2	3
β-strand	1166-1167	2	4
α-helix	1176-1178	3
α-helix	1181-1186	6
β-strand	1188-1189	2	4
α-helix	1191-1206	16
α-helix	1210-1211	2
α-helix	1218-1226	9
α-helix	1231-1234	4
α-helix	1239-1248	10
α-helix	1253-1255	3
α-helix	1257-1258	2
α-helix	1259-1266	8
α-helix	1267-1269	3
α-helix	1274-1277	4

Chain B: 20 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	983-985	3
α-helix	990-992	3
β-strand	993	1	5
α-helix	996-998	3
β-strand	999-1007	9	5
β-strand	1012-1022	11	5
β-strand	1025-1035	11	5
α-helix	1041-1054	14
β-strand	1062	1	6
α-helix	1063-1064	2
β-strand	1065-1069	5	5
β-strand	1075-1080	6	5
β-strand	1086	1	6
α-helix	1087-1093	7
α-helix	1109-1128	20
β-strand	1131-1132	2	7
α-helix	1138-1140	3
β-strand	1141-1143	3	6
β-strand	1149-1151	3	6
β-strand	1158-1159	2	7
β-strand	1166-1167	2	8
α-helix	1176-1178	3
α-helix	1181-1186	6
β-strand	1188-1189	2	8
α-helix	1191-1206	16
α-helix	1210-1211	2
α-helix	1218-1226	9
α-helix	1231-1234	4
α-helix	1239-1248	10
α-helix	1253-1255	3
α-helix	1257-1258	2
α-helix	1259-1266	8
α-helix	1267-1269	3
α-helix	1274-1277	4

Chain C: 19 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	983-986	4
β-strand	993	1	9
α-helix	996-998	3
β-strand	999-1007	9	9
β-strand	1012-1019	8	9
β-strand	1027-1034	8	9
α-helix	1041-1054	14
β-strand	1062	1	10
α-helix	1063-1064	2
β-strand	1065-1069	5	9
β-strand	1076-1080	5	9
β-strand	1086	1	10
α-helix	1087-1093	7
α-helix	1109-1128	20
β-strand	1131-1132	2	11
α-helix	1138-1140	3
β-strand	1141-1143	3	10
β-strand	1149-1151	3	10
β-strand	1158-1159	2	11
β-strand	1166-1167	2	12
α-helix	1176-1178	3
α-helix	1181-1186	6
β-strand	1188-1189	2	12
α-helix	1191-1206	16
α-helix	1210-1211	2
α-helix	1218-1226	9
α-helix	1231-1234	4
α-helix	1239-1248	10
α-helix	1253-1255	3
α-helix	1257-1258	2
α-helix	1259-1264	6
α-helix	1267-1269	3
α-helix	1274-1277	4

Chain D: 20 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	983-985	3
α-helix	990-992	3
β-strand	993	1	13
α-helix	996-998	3
β-strand	999-1007	9	13
β-strand	1012-1019	8	13
β-strand	1027-1035	9	13
α-helix	1041-1055	15
β-strand	1062	1	14
α-helix	1063-1064	2
β-strand	1065-1069	5	13
β-strand	1075-1080	6	13
β-strand	1086	1	14
α-helix	1087-1093	7
α-helix	1109-1128	20
β-strand	1131-1132	2	15
α-helix	1138-1140	3
β-strand	1141-1143	3	14
β-strand	1149-1151	3	14
β-strand	1158-1159	2	15
β-strand	1166-1167	2	16
α-helix	1176-1178	3
α-helix	1181-1186	6
β-strand	1188-1189	2	16
α-helix	1191-1206	16
α-helix	1210-1211	2
α-helix	1218-1226	9
α-helix	1231-1234	4
α-helix	1239-1248	10
α-helix	1253-1255	3
α-helix	1257-1258	2
α-helix	1259-1266	8
α-helix	1267-1269	3
α-helix	1274-1277	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Insulin-like growth factor 1 receptor	A, B, C, D	protein	308	Homo sapiens	P08069 (AlphaFold model)

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

>2ZM3_1 Insulin-like growth factor 1 receptor (chains A, B, C, D)
GSFSAADVYVPDEWEVAREKITMSRELGQGSFGMVYEGVAKGVVKDEPETRVAIKTVNEA
ASMRERIEFLNEASVMKEFNCHHVVRLLGVVSQGQPTLVIMELMTRGDLKSYLRSLRPEM
ENNPVLAPPSLSKMIQMAGEIADGMAYLNANKFVHRDLAARNCMVAEDFTVKIGDFGMTR
DIYETDYYRKGGKGLLPVRWMSPESLKDGVFTTYSDVWSFGVVLWEIATLAEQPYQGLSN
EQVLRFVMEGGLLDKPDNCPDMLFELMRMCWQYNPKMRPSFLEIISSIKEEMEPGFREVS
FYYSEENK

Ligands and cofactors

ID	Name	Formula	Copies
575	(4Z)-6-bromo-4-({[4-(pyrrolidin-1-ylmethyl)phenyl]amino}methylidene)isoquinolin…	C21 H20 Br N3 O2	4

Primary citation

Lead identification to generate isoquinolinedione inhibitors of insulin-like growth factor receptor (IGF-1R) for potential use in cancer treatment. Mayer, S.C., Banker, A.L., Boschelli, F. et al. Bioorg Med Chem Lett (2008) 18:3641-3645. DOI 10.1016/j.bmcl.2008.04.044 · PubMed

Other PDB entries of the same protein (UniProt P08069 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1P4O 1.5 Å, Structure of Apo unactivated IGF-1R KInase domain at 1.5A resolution.
8PYN 1.71 Å, Human IGF1R with inhibitor 56
3LW0 1.79 Å, IGF-1RK in complex with ligand MSC1609119A-1
5FXS 1.9 Å, IGFR-1R complex with a pyrimidine inhibitor.
2OJ9 2.0 Å, Structure of IGF-1R kinase domain complexed with a benzimidazole inhibitor
3I81 2.08 Å, Crystal structure of insulin-like growth factor 1 receptor (IGF-1R-WT) complex with…
1JQH 2.1 Å, IGF-1 receptor kinase domain
1K3A 2.1 Å, Structure of the Insulin-like Growth Factor 1 Receptor Kinase
3O23 2.1 Å, Human unphosphorylated IGF1-R Kinase domain in complex with an hydantoin inhibitor
4D2R 2.1 Å, Human IGF in complex with a Dyrk1B inhibitor
3NW7 2.11 Å, Crystal structure of insulin-like growth factor 1 receptor (IGF-1R-WT) complex with a…
3NW5 2.14 Å, Crystal structure of insulin-like growth factor 1 receptor (IGF-1R-WT) complex with a…

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