scPDB - 4aoj entry

Protein Data Bank Entry:

PDB ID : 4aoj

Resolution :2.750 Å

Experimental Method : X-ray

Deposition Date : 2012-03-28

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	High affinity nerve growth factor receptor
ID:	NTRK1_HUMAN
AC:	P04629
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.7.10.1

Chains:

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

Ligand binding site composition:

B-Factor:	47.823
Number of residues:	33
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.147	529.875

% Hydrophobic	% Polar
51.59	48.41
According to VolSite

Ligand :

HET Code:	V4Z
Formula:	C17H19ClFN7O
Molecular weight:	391.830 g/mol
DrugBank ID:	-
Buried Surface Area:	68.99 %
Polar Surface area:	100.64 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	3
Rings:	3
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
31.1695	65.0872	24.7476

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
C17	CB	LEU- 516	3.74	0	Hydrophobic	false
CL1	CD2	LEU- 516	3.82	0	Hydrophobic	false
C10	CZ	PHE- 521	4.24	0	Hydrophobic	false
C3	CG1	VAL- 524	3.83	0	Hydrophobic	false
C10	CG2	VAL- 524	3.56	0	Hydrophobic	false
C3	CB	ALA- 542	4.09	0	Hydrophobic	false
C3	CB	LYS- 544	4.42	0	Hydrophobic	false
C1	CG1	VAL- 573	4.01	0	Hydrophobic	false
C3	CD1	PHE- 589	3.77	0	Hydrophobic	false
N7	O	GLU- 590	2.69	157.07	H-Bond (Ligand Donor)	false
CL1	CE1	TYR- 591	4.05	0	Hydrophobic	false
N1	O	MET- 592	3.28	134.58	H-Bond (Ligand Donor)	false
N6	N	MET- 592	2.77	169.3	H-Bond (Protein Donor)	false
C12	CD2	LEU- 657	4.08	0	Hydrophobic	false
C13	CD1	LEU- 657	3.6	0	Hydrophobic	false
C2	CD1	LEU- 657	4.06	0	Hydrophobic	false
C14	CG	LEU- 657	3.57	0	Hydrophobic	false
F1	CB	ASP- 668	3.8	0	Hydrophobic	false