scPDB - 3c1x entry

Protein Data Bank Entry:

PDB ID : 3c1x

Resolution :2.170 Å

Experimental Method : X-ray

Deposition Date : 2008-01-24

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Hepatocyte growth factor receptor
ID:	MET_HUMAN
AC:	P08581
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.7.10.1

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	58.640
Number of residues:	40
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.315	442.125

% Hydrophobic	% Polar
68.70	31.30
According to VolSite

Ligand :

HET Code:	CKK
Formula:	C27H29F2N7O3
Molecular weight:	537.561 g/mol
DrugBank ID:	-
Buried Surface Area:	62.53 %
Polar Surface area:	129.69 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	4
Rings:	5
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	2
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
0.193282	8.12177	54.5796

Binding mode :

What is Poseview ?

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Image generated by PoseView

Protein

Binding Site

Ligand

Interaction pattern

hydrophobic (CA)

aromatic (CZ)

hydrogen bond acceptor (O)

hydrogen bond acceptor/donor (OG)

hydrogen bond donor (N)

positively ionized (NZ)

negatively ionized (OD1)

metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT

Ligand	Protein		Interaction
Atom	Atom	Residue	Distance (Å)	Angle (°)	Type
F18	CG1	VAL- 1092	3.21	0	Hydrophobic	false
F18	CD	LYS- 1110	3.36	0	Hydrophobic	false
N11	OE2	GLU- 1127	2.63	159.75	H-Bond (Ligand Donor)	false
C8	SD	MET- 1131	3.52	0	Hydrophobic	false
C6	CG	MET- 1131	3.9	0	Hydrophobic	false
F1	CE2	PHE- 1134	4.41	0	Hydrophobic	false
C5	CG1	VAL- 1139	4.19	0	Hydrophobic	false
C19	CD2	LEU- 1140	3.6	0	Hydrophobic	false
C17	CD1	LEU- 1157	3.51	0	Hydrophobic	false
N26	N	MET- 1160	3.08	143.53	H-Bond (Protein Donor)	false
C38	CB	ASP- 1164	4.14	0	Hydrophobic	false
N39	OD2	ASP- 1164	3.02	175.83	H-Bond (Ligand Donor)	false
N39	OD2	ASP- 1164	3.02	0	Ionic (Ligand Cationic)	false
F1	CD2	LEU- 1195	4.23	0	Hydrophobic	false
C2	CD1	LEU- 1195	4.4	0	Hydrophobic	false
F1	CE2	PHE- 1200	3.72	0	Hydrophobic	false
C19	CG	MET- 1211	4.47	0	Hydrophobic	false
C20	SD	MET- 1211	3.91	0	Hydrophobic	false
C38	SD	MET- 1211	3.65	0	Hydrophobic	false
F1	CG1	VAL- 1220	4.08	0	Hydrophobic	false
C19	CB	ALA- 1221	4.13	0	Hydrophobic	false
C3	CB	ASP- 1222	3.58	0	Hydrophobic	false
C7	CB	ASP- 1222	3.8	0	Hydrophobic	false
O10	N	ASP- 1222	2.91	145.08	H-Bond (Protein Donor)	false
F18	CE1	PHE- 1223	3.89	0	Hydrophobic	false
C36	CE2	PHE- 1223	4.43	0	Hydrophobic	false
C38	CG	PHE- 1223	4.22	0	Hydrophobic	false