scPDB - 4iwd entry

Protein Data Bank Entry:

PDB ID : 4iwd

Resolution :1.990 Å

Experimental Method : X-ray

Deposition Date : 2013-01-23

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:	20.471
Number of residues:	36
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.789	442.125

% Hydrophobic	% Polar
51.15	48.85
According to VolSite

Ligand :

HET Code:	1JC
Formula:	C29H29N6O3S
Molecular weight:	541.644 g/mol
DrugBank ID:	-
Buried Surface Area:	62.86 %
Polar Surface area:	131.82 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	2
Rings:	6
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
-3.79179	-5.184	-14.8507

Binding mode :

What is Poseview ?

2D View
3D View

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
C4	CD1	ILE- 1084	3.83	0	Hydrophobic	false
C27	CD	ARG- 1086	4.46	0	Hydrophobic	false
C28	CB	HIS- 1088	4.19	0	Hydrophobic	false
C8	CG1	VAL- 1092	4.18	0	Hydrophobic	false
C13	CG2	VAL- 1092	3.9	0	Hydrophobic	false
C3	CB	ALA- 1108	4.29	0	Hydrophobic	false
C10	CD2	LEU- 1140	3.89	0	Hydrophobic	false
C10	CD1	LEU- 1157	3.77	0	Hydrophobic	false
N	N	MET- 1160	2.82	164.04	H-Bond (Protein Donor)	false
C23	CG	ARG- 1208	3.9	0	Hydrophobic	false
DuAr	CZ	ARG- 1208	3.77	159.07	Pi/Cation	false
N15	OD1	ASN- 1209	2.66	133.82	H-Bond (Ligand Donor)	false
C3	CE	MET- 1211	3.88	0	Hydrophobic	false
C4	SD	MET- 1211	4.08	0	Hydrophobic	false
C8	CE	MET- 1211	3.54	0	Hydrophobic	false
C13	CE	MET- 1211	3.57	0	Hydrophobic	false
C10	CB	ALA- 1221	3.96	0	Hydrophobic	false
C11	CB	ASP- 1222	4.4	0	Hydrophobic	false
C14	CB	ASP- 1222	4.08	0	Hydrophobic	false