scPDB - 3toh entry

Protein Data Bank Entry:

PDB ID : 3toh

Resolution :1.120 Å

Experimental Method : X-ray

Deposition Date : 2011-09-05

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Gag-Pol polyprotein
ID:	POL_HV1BR
AC:	P03367
Organism:	Human immunodeficiency virus type 1 group M subtype B
Reign:	Viruses
TaxID:	11686
EC Number:	2.7.7.49

Chains:

Chain Name:	Percentage of Residues within binding site
A	59 %
B	41 %

Ligand binding site composition:

B-Factor:	9.996
Number of residues:	39
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.657	668.250

% Hydrophobic	% Polar
38.89	61.11
According to VolSite

Ligand :

HET Code:	079
Formula:	C31H40N3O5
Molecular weight:	534.666 g/mol
DrugBank ID:	-
Buried Surface Area:	57.2 %
Polar Surface area:	135.53 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	5
Rings:	3
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	14

Mass center Coordinates

X	Y	Z
20.1521	33.0885	15.3979

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
C27	CD2	LEU- 23	4.47	0	Hydrophobic	false
C25	CD2	LEU- 23	4.05	0	Hydrophobic	false
C21	CD2	LEU- 23	3.92	0	Hydrophobic	false
O4	OD2	ASP- 25	2.64	172.71	H-Bond (Ligand Donor)	false
O4	OD1	ASP- 25	2.6	146.56	H-Bond (Protein Donor)	false
N2	O	GLY- 27	3.17	148.89	H-Bond (Ligand Donor)	false
C11	CB	ALA- 28	4.09	0	Hydrophobic	false
O1	N	ASP- 29	2.86	166.37	H-Bond (Protein Donor)	false
C11	CG2	VAL- 32	4.27	0	Hydrophobic	false
C12	CG2	VAL- 32	4.35	0	Hydrophobic	false
C12	CD1	ILE- 47	4.2	0	Hydrophobic	false
N1	O	GLY- 48	3.09	146.09	H-Bond (Ligand Donor)	false
C11	CG1	ILE- 50	4.37	0	Hydrophobic	false
C31	CB	ILE- 50	4.5	0	Hydrophobic	false
C17	CG1	ILE- 50	4.37	0	Hydrophobic	false
C18	CG	PRO- 81	3.91	0	Hydrophobic	false
C19	CB	PRO- 81	3.92	0	Hydrophobic	false
C7	CB	PRO- 81	3.77	0	Hydrophobic	false
C30	CG	PRO- 81	3.35	0	Hydrophobic	false
C28	CG2	VAL- 82	4.2	0	Hydrophobic	false
C19	CB	VAL- 82	4.01	0	Hydrophobic	false
C21	CG1	VAL- 82	3.48	0	Hydrophobic	false
C11	CD1	ILE- 84	3.78	0	Hydrophobic	false
C31	CD1	ILE- 84	4.34	0	Hydrophobic	false
C25	CD1	ILE- 84	3.97	0	Hydrophobic	false
C15	CG2	ILE- 84	4	0	Hydrophobic	false
O2	O	HOH- 226	3.1	122.9	H-Bond (Protein Donor)	false
O3	O	HOH- 243	2.79	179.94	H-Bond (Protein Donor)	false