scPDB - 3liv entry

Protein Data Bank Entry:

PDB ID : 3liv

Resolution :2.590 Å

Experimental Method : X-ray

Deposition Date : 2010-01-25

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Protease
ID:	Q82134_9DELA
AC:	Q82134
Organism:	Human T-lymphotropic virus 1
Reign:	Viruses
TaxID:	11908
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	49 %
B	51 %

Ligand binding site composition:

B-Factor:	30.885
Number of residues:	42
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.333	1083.375

% Hydrophobic	% Polar
49.84	50.16
According to VolSite

Ligand :

HET Code:	E16
Formula:	C36H54N5O5S
Molecular weight:	668.909 g/mol
DrugBank ID:	-
Buried Surface Area:	60.89 %
Polar Surface area:	180.77 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
20.3942	33.3915	25.8507

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
CAX	CD	ARG- 10	4.45	0	Hydrophobic	false
CAT	CD	ARG- 10	3.68	0	Hydrophobic	false
CAI	CD2	LEU- 30	3.23	0	Hydrophobic	false
OAN	OD2	ASP- 32	2.77	152.37	H-Bond (Protein Donor)	false
OAO	OD2	ASP- 32	3.04	122.19	H-Bond (Protein Donor)	false
OAO	OD1	ASP- 32	2.75	156.95	H-Bond (Ligand Donor)	false
OAO	OD2	ASP- 32	3.01	132.76	H-Bond (Ligand Donor)	false
NBC	O	GLY- 34	3.03	163.65	H-Bond (Ligand Donor)	false
CAB	CB	ALA- 35	4.15	0	Hydrophobic	false
CAC	CB	ALA- 35	4.16	0	Hydrophobic	false
CG2	CB	ALA- 35	3.78	0	Hydrophobic	false
NAJ	OD2	ASP- 36	2.94	0	Ionic (Ligand Cationic)	false
OAK	N	ASP- 36	3.24	163.42	H-Bond (Protein Donor)	false
CG2	CG2	VAL- 39	4.41	0	Hydrophobic	false
CAC	CG2	VAL- 39	4.45	0	Hydrophobic	false
CAD	CG2	VAL- 39	4.1	0	Hydrophobic	false
CG1	CG1	VAL- 56	3.41	0	Hydrophobic	false
CAA	CG1	VAL- 56	3.66	0	Hydrophobic	false
CAD	CG1	VAL- 56	3.78	0	Hydrophobic	false
N	O	LEU- 57	2.99	151.32	H-Bond (Ligand Donor)	false
CAY	CD1	LEU- 57	3.76	0	Hydrophobic	false
CG1	CB	ALA- 59	3.6	0	Hydrophobic	false
CG2	CB	ALA- 59	4.44	0	Hydrophobic	false
CAR	CB	ALA- 59	3.77	0	Hydrophobic	false
CAD	CB	ALA- 59	3.72	0	Hydrophobic	false
CAD	CZ	PHE- 67	4.08	0	Hydrophobic	false
CAG	CD1	LEU- 91	4.06	0	Hydrophobic	false
CAC	CD1	LEU- 91	3.87	0	Hydrophobic	false
CAD	CD1	LEU- 91	4.12	0	Hydrophobic	false
SBE	CZ3	TRP- 98	4.07	0	Hydrophobic	false
CAP	CZ2	TRP- 98	3.31	0	Hydrophobic	false
CG2	CD1	ILE- 100	4.36	0	Hydrophobic	false
CAR	CD1	ILE- 100	4.3	0	Hydrophobic	false
SBE	CD1	ILE- 100	4.46	0	Hydrophobic	false
CAB	CD1	ILE- 100	4.34	0	Hydrophobic	false
CAV	CD1	ILE- 100	3.72	0	Hydrophobic	false
NBB	O	HOH- 137	2.77	151.27	H-Bond (Ligand Donor)	false