4R1V: Hepatocyte growth factor receptor

Identification and optimization of pyridazinones as potent and selective c-Met kinase inhibitors. Determined by X-ray diffraction at 1.2 Å resolution. Released 18 Mar 2015.

Method: X-ray diffraction
Resolution: 1.2 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,770
Mol. weight: 33.74 kDa
Ligands: GBL, 3E8
Released: 18 Mar 2015

Explore 4R1V in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4R1V contains 21 α-helices and 13 β-strands across 1 chain. 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: 21 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	1060-1066	7
α-helix	1067-1069	3
β-strand	1070	1	1
α-helix	1073-1075	3
β-strand	1076-1087	12	1
β-strand	1090-1098	9	1
β-strand	1104-1111	8	1
α-helix	1118-1133	16
β-strand	1136	1	2
β-strand	1139	1	2
α-helix	1140-1142	3
β-strand	1144-1146	3	1
β-strand	1154-1158	5	1
β-strand	1164	1	2
α-helix	1165-1170	6
α-helix	1178-1197	20
α-helix	1207-1209	3
β-strand	1210-1212	3	2
β-strand	1218-1220	3	2
α-helix	1224-1226	3
α-helix	1232-1234	3
β-strand	1236-1237	2	3
β-strand	1244-1245	2	3
α-helix	1247-1249	3
α-helix	1252-1257	6
α-helix	1262-1277	16
α-helix	1281-1282	2
α-helix	1289-1291	3
α-helix	1292-1297	6
α-helix	1302-1305	4
α-helix	1310-1319	10
α-helix	1324-1326	3
α-helix	1328-1329	2
α-helix	1330-1342	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Hepatocyte growth factor receptor	A	protein	291	Homo sapiens	P08581 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4R1V_1 Hepatocyte growth factor receptor (chains A)
LSALNPELVQAVQHVVIGPSSLIVHFNEVIGRGHFGCVYHGTLLDNDGKKIHCAVKSLNR
ITDIGEVSQFLTEGIIMKDFSHPNVLSLLGICLRSEGSPLVVLPYMKHGDLRNFIRNETH
NPTVKDLIGFGLQVAKGMKYLASKKFVHRDLAARNCMLDEKFTVKVADFGLARDMYDKEY
YSVHNKTGAKLPVKWMALESLQTQKFTTKSDVWSFGVLLWELMTRGAPPYPDVNTFDITV
YLLQGRRLLQPEYCPDPLYEVMLKCWHPKAEMRPSFSELVSRISAIFSTFI

Ligands and cofactors

ID	Name	Formula	Copies
GBL	Gamma-butyrolactone	C4 H6 O2	3
3E8	3-[1-(3-{5-[(1-methylpiperidin-4-yl)methoxy]pyrimidin-2-yl}benzyl)-6-oxo-1,6-di…	C29 H28 N6 O2	1

Primary citation

Identification and optimization of pyridazinones as potent and selective c-Met kinase inhibitors. Dorsch, D., Schadt, O., Stieber, F. et al. Bioorg Med Chem Lett (2015) 25:1597-1602. DOI 10.1016/j.bmcl.2015.02.002 · PubMed

Other PDB entries of the same protein (UniProt P08581 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9T6K 1.13 Å, Crystal structure of wild-type c-MET bound by glumetinib.
9T0D 1.2 Å, Crystal structure of wild-type c-MET bound by glesatinib
9SXJ 1.31 Å, Crystal structure of wild-type c-MET bound by capmatinib.
3BUX 1.35 Å, Crystal structure of c-Cbl-TKB domain complexed with its binding motif in c-Met
3F66 1.4 Å, Human c-Met Kinase in complex with quinoxaline inhibitor
3ZCL 1.4 Å, X-ray Structure of c-Met kinase in complex with inhibitor…
9T08 1.46 Å, Crystal structure of wild-type c-MET bound by sitravatinib.
3DKC 1.52 Å, Structure of MET receptor tyrosine kinase in complex with ATP
9T0B 1.54 Å, Crystal structure of D1228V c-MET bound by sitravatinib.
9C1R 1.59 Å, Crystal structure of mutant cMET D1228N kinase domain in complex with inhibitor compound…
3Q6U 1.6 Å, Structure of the apo MET receptor kinase in the dually-phosphorylated, activated state
9T3Q 1.63 Å, Crystal structure of D1228V c-MET bound by cabozantinib.

Browse structure collections

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