scPDB - 3dtw entry

Protein Data Bank Entry:

PDB ID : 3dtw

Resolution :2.900 Å

Experimental Method : X-ray

Deposition Date : 2008-07-16

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Vascular endothelial growth factor receptor 2
ID:	VGFR2_HUMAN
AC:	P35968
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.7.10.1

Chains:

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

Ligand binding site composition:

B-Factor:	40.589
Number of residues:	33
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.433	715.500

% Hydrophobic	% Polar
61.32	38.68
According to VolSite

Ligand :

HET Code:	A96
Formula:	C19H11ClF3N5O2
Molecular weight:	433.771 g/mol
DrugBank ID:	DB07326
Buried Surface Area:	73.2 %
Polar Surface area:	92.94 Å2

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

Mass center Coordinates

X	Y	Z
25.047	3.15243	27.3161

Binding mode :

What is Poseview ?

2D View
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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
CL24	CG1	VAL- 848	3.8	0	Hydrophobic	false
CL24	CB	ALA- 866	3.71	0	Hydrophobic	false
C16	CD	LYS- 868	4.46	0	Hydrophobic	false
CL24	CB	LYS- 868	3.78	0	Hydrophobic	false
C17	CB	LYS- 868	3.76	0	Hydrophobic	false
C27	CG	GLU- 885	3.49	0	Hydrophobic	false
C28	CG2	ILE- 888	4.4	0	Hydrophobic	false
C27	CG	LEU- 889	4.22	0	Hydrophobic	false
F39	CD2	LEU- 889	4.3	0	Hydrophobic	false
C16	CD1	LEU- 889	4.04	0	Hydrophobic	false
C31	CD2	LEU- 889	3.58	0	Hydrophobic	false
F39	CD1	ILE- 892	3.66	0	Hydrophobic	false
F39	CG1	VAL- 898	3.48	0	Hydrophobic	false
C31	CG1	VAL- 899	4.45	0	Hydrophobic	false
C17	CG1	VAL- 914	3.99	0	Hydrophobic	false
N10	OG1	THR- 916	3.16	167.34	H-Bond (Ligand Donor)	false
CL24	CG2	THR- 916	4.28	0	Hydrophobic	false
C17	CG2	THR- 916	3.34	0	Hydrophobic	false
N1	N	CYS- 919	3.08	155.48	H-Bond (Protein Donor)	false
F38	CD1	LEU- 1019	3.92	0	Hydrophobic	false
F39	CD2	LEU- 1019	3.82	0	Hydrophobic	false
F37	CG2	ILE- 1044	3.82	0	Hydrophobic	false
O21	N	ASP- 1046	3.45	171.82	H-Bond (Protein Donor)	false
N22	N	ASP- 1046	2.95	139.76	H-Bond (Protein Donor)	false
F37	CB	ASP- 1046	4.33	0	Hydrophobic	false
C30	CB	ASP- 1046	3.98	0	Hydrophobic	false