scPDB - 3ec0 entry

Protein Data Bank Entry:

PDB ID : 3ec0

Resolution :1.180 Å

Experimental Method : X-ray

Deposition Date : 2008-08-28

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_HV2RO
AC:	P04584
Organism:	Human immunodeficiency virus type 2 subtype A
Reign:	Viruses
TaxID:	11720
EC Number:	3.4.23.47

Chains:

Chain Name:	Percentage of Residues within binding site
A	50 %
B	50 %

Ligand binding site composition:

B-Factor:	13.209
Number of residues:	45
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	5
Water Molecules:	0
Cofactors:
Metals:	CL CL ZN ZN

Cavity properties

Ligandability	Volume (Å3)
0.824	688.500

% Hydrophobic	% Polar
40.20	59.80
According to VolSite

Ligand :

HET Code:	GRL
Formula:	C29H40N2O7S
Molecular weight:	560.702 g/mol
DrugBank ID:	-
Buried Surface Area:	72.65 %
Polar Surface area:	133.78 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	3
Rings:	4
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
20.4092	11.0627	17.8036

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
C23	CD2	LEU- 23	4.31	0	Hydrophobic	false
C25	CD2	LEU- 23	4.02	0	Hydrophobic	false
O31	OD2	ASP- 25	2.51	174.85	H-Bond (Ligand Donor)	false
C32	CB	ALA- 28	4.43	0	Hydrophobic	false
C43	CB	ALA- 28	3.71	0	Hydrophobic	false
C3	CB	ASP- 30	3.68	0	Hydrophobic	false
O2	OD2	ASP- 30	2.71	172.42	H-Bond (Ligand Donor)	false
O2	N	ASP- 30	3.11	136.48	H-Bond (Protein Donor)	false
C44	CD1	ILE- 32	3.49	0	Hydrophobic	false
C45	CB	VAL- 47	4.13	0	Hydrophobic	false
C3	CG1	VAL- 47	4.16	0	Hydrophobic	false
C11	CD1	ILE- 50	4.04	0	Hydrophobic	false
C35	CG1	ILE- 50	4.41	0	Hydrophobic	false
C3	CE	MET- 76	4.04	0	Hydrophobic	false
C28	CG	PRO- 81	3.85	0	Hydrophobic	false
C26	CG2	ILE- 82	3.55	0	Hydrophobic	false
C42	CD1	ILE- 84	3.94	0	Hydrophobic	false
C23	CD1	ILE- 84	3.9	0	Hydrophobic	false
C36	CD2	LEU- 123	3.87	0	Hydrophobic	false
O31	OD1	ASP- 125	2.59	167.16	H-Bond (Protein Donor)	false
N21	O	GLY- 127	3.11	158.93	H-Bond (Ligand Donor)	false
C16	CB	ALA- 128	4.08	0	Hydrophobic	false
O1	N	ASP- 129	2.77	170.12	H-Bond (Protein Donor)	false
C14	CB	ASP- 129	4.35	0	Hydrophobic	false
C1	CB	ASP- 129	4.15	0	Hydrophobic	false
C16	CB	ASP- 130	4.31	0	Hydrophobic	false
C16	CD1	ILE- 132	4.25	0	Hydrophobic	false
C12	CG1	VAL- 147	3.66	0	Hydrophobic	false
C41	CD1	ILE- 150	3.96	0	Hydrophobic	false
C36	CD1	ILE- 182	3.82	0	Hydrophobic	false
C11	CD1	ILE- 184	4.1	0	Hydrophobic	false
C36	CG2	ILE- 184	4.03	0	Hydrophobic	false