5HTI: C-Met kinase domain

Crystal structure of c-Met kinase domain in complex with LXM108. Determined by X-ray diffraction at 1.66 Å resolution. Released 1 Feb 2017.

Method: X-ray diffraction
Resolution: 1.66 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,571
Mol. weight: 36.62 kDa
Ligands: 66L
Released: 1 Feb 2017

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

Secondary structure: helices and β-sheets

5HTI contains 20 α-helices and 12 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: 20 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	1055-1057	3
α-helix	1060-1067	8
β-strand	1070	1	1
α-helix	1073-1075	3
β-strand	1076-1086	11	1
β-strand	1090-1098	9	1
β-strand	1104-1112	9	1
α-helix	1118-1131	14
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
β-strand	1236	1	3
β-strand	1245	1	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	319	Homo sapiens	P08581 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5HTI_1 Hepatocyte growth factor receptor (chains A)
MGSSHHHHHHGDSDISSPLLQNTVHIDLSALNPELVQAVQHVVIGPSSLIVHFNEVIGRG
HFGCVYHGTLLDNDGKKIHCAVKSLNRITDIGEVSQFLTEGIIMKDFSHPNVLSLLGICL
RSEGSPLVVLPYMKHGDLRNFIRNETHNPTVKDLIGFGLQVAKGMKYLASKKFVHRDLAA
RNCMLDEKFTVKVADFGLARDMYDKEYYSVHNKTGAKLPVKWMALESLQTQKFTTKSDVW
SFGVLLWELMTRGAPPYPDVNTFDITVYLLQGRRLLQPEYCPDPLYEVMLKCWHPKAEMR
PSFSELVSRISAIFSTFIG

Ligands and cofactors

ID	Name	Formula	Copies
66L	N-[3-fluoro-4-({7-[2-(morpholin-4-yl)ethoxy]-1,6-naphthyridin-4-yl}oxy)phenyl]-…	C31 H29 F2 N5 O5	1

Primary citation

Crystal structure of c-Met kinase domain in complex with LXM108. Xu, Y.C., Long, Y. To be published.

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
4R1V 1.2 Å, Identification and optimization of pyridazinones as potent and selective c-Met kinase…
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

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