scPDB - 4at3 entry

Protein Data Bank Entry:

PDB ID : 4at3

Resolution :1.770 Å

Experimental Method : X-ray

Deposition Date : 2012-05-03

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	BDNF/NT-3 growth factors receptor
ID:	NTRK2_HUMAN
AC:	Q16620
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:	25.448
Number of residues:	33
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.027	826.875

% Hydrophobic	% Polar
54.69	45.31
According to VolSite

Ligand :

HET Code:	LTI
Formula:	C16H18N4O2S2
Molecular weight:	362.470 g/mol
DrugBank ID:	-
Buried Surface Area:	67.85 %
Polar Surface area:	161.17 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	3
Rings:	3
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	3

Mass center Coordinates

X	Y	Z
9.45179	-27.228	-15.8249

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
C14	CB	PHE- 565	3.8	0	Hydrophobic	false
C13	CG	PHE- 565	4.09	0	Hydrophobic	false
C20	CZ	PHE- 565	3.33	0	Hydrophobic	false
C14	CG2	VAL- 568	4.4	0	Hydrophobic	false
S24	CG1	VAL- 568	4.09	0	Hydrophobic	false
S24	CB	ALA- 586	4.09	0	Hydrophobic	false
C15	CB	LYS- 588	4.26	0	Hydrophobic	false
C23	CG2	VAL- 617	4.15	0	Hydrophobic	false
C17	CG1	VAL- 617	4.27	0	Hydrophobic	false
C17	CD2	PHE- 633	3.9	0	Hydrophobic	false
C16	CZ	PHE- 633	3.59	0	Hydrophobic	false
C15	CE1	PHE- 633	3.61	0	Hydrophobic	false
N12	O	GLU- 634	2.97	164.04	H-Bond (Ligand Donor)	false
N6	O	MET- 636	3.32	134.25	H-Bond (Ligand Donor)	false
O11	N	MET- 636	2.74	169.96	H-Bond (Protein Donor)	false
C20	CD2	LEU- 699	3.93	0	Hydrophobic	false
S24	CD1	LEU- 699	4.37	0	Hydrophobic	false
C21	CG	LEU- 699	3.66	0	Hydrophobic	false
C19	CD1	LEU- 699	3.8	0	Hydrophobic	false
C22	CB	ASP- 710	4.23	0	Hydrophobic	false
O8	O	HOH- 2079	2.87	179.98	H-Bond (Protein Donor)	false