scPDB - 3nyg entry

Protein Data Bank Entry:

PDB ID : 3nyg

Resolution :1.450 Å

Experimental Method : X-ray

Deposition Date : 2010-07-15

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_HV1A2
AC:	P03369
Organism:	Human immunodeficiency virus type 1 group M subtype B
Reign:	Viruses
TaxID:	11685
EC Number:	3.4.23.16

Chains:

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

Ligand binding site composition:

B-Factor:	17.099
Number of residues:	48
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	2
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.877	803.250

% Hydrophobic	% Polar
42.02	57.98
According to VolSite

Ligand :

HET Code:	2NC
Formula:	C35H69N11O8
Molecular weight:	771.991 g/mol
DrugBank ID:	-
Buried Surface Area:	67.5 %
Polar Surface area:	332.16 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	12
Rings:	0
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	2
Rule of Five Violation:	3
Rotatable Bonds:	30

Mass center Coordinates

X	Y	Z
5.31402	-1.04339	13.7525

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
CD4	CD	ARG- 8	4.14	0	Hydrophobic	false
CG	CD2	LEU- 23	4.21	0	Hydrophobic	false
CG3	CD2	LEU- 23	3.69	0	Hydrophobic	false
N3	OD2	ASP- 25	2.84	149.62	H-Bond (Ligand Donor)	false
N3	OD2	ASP- 25	2.84	0	Ionic (Ligand Cationic)	false
N2	O	GLY- 27	2.89	161.56	H-Bond (Ligand Donor)	false
N4	O	GLY- 27	3	165.36	H-Bond (Ligand Donor)	false
CG21	CB	ALA- 28	4.04	0	Hydrophobic	false
CD1	CB	ALA- 28	4.17	0	Hydrophobic	false
CB4	CB	ALA- 28	3.85	0	Hydrophobic	false
O1	N	ASP- 29	2.98	164.05	H-Bond (Protein Donor)	false
O4	N	ASP- 29	3.03	160.51	H-Bond (Protein Donor)	false
CB	CB	ASP- 29	4.3	0	Hydrophobic	false
N6	OD2	ASP- 29	3.38	156.19	H-Bond (Ligand Donor)	false
CD1	CB	ASP- 30	3.83	0	Hydrophobic	false
OE1	N	ASP- 30	2.9	158.91	H-Bond (Protein Donor)	false
NE2	OD2	ASP- 30	2.69	172.11	H-Bond (Ligand Donor)	false
CG21	CG2	VAL- 32	4.19	0	Hydrophobic	false
CG4	CG2	VAL- 32	4.13	0	Hydrophobic	false
CD1	CG2	VAL- 32	4.19	0	Hydrophobic	false
CG1	CD1	ILE- 47	3.95	0	Hydrophobic	false
CG4	CD1	ILE- 47	4	0	Hydrophobic	false
N	O	GLY- 48	3.04	128.54	H-Bond (Ligand Donor)	false
N1	O	GLY- 48	2.96	152.88	H-Bond (Ligand Donor)	false
N5	O	GLY- 48	2.95	163.88	H-Bond (Ligand Donor)	false
O5	N	GLY- 48	2.95	171.54	H-Bond (Protein Donor)	false
CB1	CG2	ILE- 50	4.26	0	Hydrophobic	false
CG21	CD1	ILE- 50	3.75	0	Hydrophobic	false
CE	CG1	ILE- 50	3.92	0	Hydrophobic	false
CE1	CB	ILE- 50	4.48	0	Hydrophobic	false
CG4	CD1	ILE- 50	3.82	0	Hydrophobic	false
CH3	CB	PRO- 81	3.79	0	Hydrophobic	false
CD	CB	PRO- 81	4.48	0	Hydrophobic	false
CE	CG	PRO- 81	4.22	0	Hydrophobic	false
CE1	CG	PRO- 81	3.9	0	Hydrophobic	false
CG	CB	VAL- 82	4.24	0	Hydrophobic	false
CD	CG2	VAL- 82	4.25	0	Hydrophobic	false
CE	CB	VAL- 82	4.33	0	Hydrophobic	false
CE1	CG2	VAL- 82	4.4	0	Hydrophobic	false
CG21	CD1	ILE- 84	3.74	0	Hydrophobic	false
CB3	CD1	ILE- 84	4.03	0	Hydrophobic	false
CE1	CD1	ILE- 84	3.81	0	Hydrophobic	false
CB2	CG2	ILE- 84	3.99	0	Hydrophobic	false
CB4	CD1	ILE- 84	4.01	0	Hydrophobic	false