3F66: Human c-Met Kinase

Human c-Met Kinase in complex with quinoxaline inhibitor. Determined by X-ray diffraction at 1.4 Å resolution. Released 23 Dec 2008.

Method: X-ray diffraction
Resolution: 1.4 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,160
Mol. weight: 68.92 kDa
Ligands: GBL, IHX
Released: 23 Dec 2008

Explore 3F66 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3F66 contains 39 α-helices and 22 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: 20 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	1055-1057	3
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	1090-1097	8	1
β-strand	1105-1112	8	1
α-helix	1118-1132	15
β-strand	1139	1	2
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	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	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

Chain B: 19 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	1063-1066	4
β-strand	1070	1	4
α-helix	1073-1075	3
β-strand	1076-1086	11	4
β-strand	1091-1097	7	4
β-strand	1105-1111	7	4
α-helix	1121-1133	13
β-strand	1139	1	5
β-strand	1144-1146	3	4
β-strand	1154-1157	4	4
β-strand	1164	1	5
α-helix	1165-1170	6
α-helix	1178-1197	20
α-helix	1207-1209	3
β-strand	1210-1212	3	5
β-strand	1218-1220	3	5
α-helix	1224-1226	3
α-helix	1232-1234	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	1330-1341	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Hepatocyte growth factor receptor	A, B	protein	298	Homo sapiens	P08581 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3F66_1 Hepatocyte growth factor receptor (chains A, B)
HIDLSALNPELVQAVQHVVIGPSSLIVHFNEVIGRGHFGCVYHGTLLDNDGKKIHCAVKS
LNRITDIGEVSQFLTEGIIMKDFSHPNVLSLLGICLRSEGSPLVVLPYMKHGDLRNFIRN
ETHNPTVKDLIGFGLQVAKGMKYLASKKFVHRDLAARNCMLDEKFTVKVADFGLARDMYD
KEYYSVHNKTGAKLPVKWMALESLQTQKFTTKSDVWSFGVLLWELMTRGAPPYPDVNTFD
ITVYLLQGRRLLQPEYCPDPLYEVMLKCWHPKAEMRPSFSELVSRISAIFSTFIGEHY

Ligands and cofactors

ID	Name	Formula	Copies
GBL	Gamma-butyrolactone	C4 H6 O2	5
IHX	3-[3-(4-methylpiperazin-1-yl)-7-(trifluoromethyl)quinoxalin-5-yl]phenol	C20 H19 F3 N4 O	2

Water and common crystallization additives (NA) are not listed.

Primary citation

Discovery of a novel series of quinoxalines as inhibitors of c-Met kinase. Porter, J., Lumb, S., Lecomte, F. et al. Bioorg Med Chem Lett (2009) 19:397-400. DOI 10.1016/j.bmcl.2008.11.062 · 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
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
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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