scPDB - 2uy0 entry

Protein Data Bank Entry:

PDB ID : 2uy0

Resolution :1.760 Å

Experimental Method : X-ray

Deposition Date : 2007-04-02

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_HV1B1
AC:	P03366
Organism:	Human immunodeficiency virus type 1 group M subtype B
Reign:	Viruses
TaxID:	11678
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:	11.922
Number of residues:	46
Including
Standard Amino Acids:	45
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.073	975.375

% Hydrophobic	% Polar
46.02	53.98
According to VolSite

Ligand :

HET Code:	HV1
Formula:	C36H43BrN4O7
Molecular weight:	723.653 g/mol
DrugBank ID:	-
Buried Surface Area:	70.81 %
Polar Surface area:	157.29 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	5
Rings:	4
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	14

Mass center Coordinates

X	Y	Z
12.5528	22.833	5.3175

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
C21	CD2	LEU- 23	3.54	0	Hydrophobic	false
O22	OD2	ASP- 25	2.89	165.65	H-Bond (Ligand Donor)	false
N2	O	GLY- 27	3.06	160.86	H-Bond (Ligand Donor)	false
C46	CB	ALA- 28	3.82	0	Hydrophobic	false
C36	CB	ASP- 29	4.09	0	Hydrophobic	false
O39	N	ASP- 29	2.85	161.19	H-Bond (Protein Donor)	false
C45	CB	ASP- 30	4.19	0	Hydrophobic	false
C46	CG1	VAL- 32	4.32	0	Hydrophobic	false
C47	CD1	ILE- 47	3.73	0	Hydrophobic	false
C45	CD1	ILE- 47	4.39	0	Hydrophobic	false
N3	O	GLY- 48	3.03	149.12	H-Bond (Ligand Donor)	false
C6	CD1	ILE- 50	3.59	0	Hydrophobic	false
C18	CG	PRO- 81	3.54	0	Hydrophobic	false
C19	CG2	VAL- 82	3.66	0	Hydrophobic	false
C15	CD1	ILE- 84	4.01	0	Hydrophobic	false
C32	CD2	LEU- 123	3.59	0	Hydrophobic	false
N4	O	GLY- 127	3.29	167.89	H-Bond (Ligand Donor)	false
O14	O	GLY- 127	2.91	148.22	H-Bond (Ligand Donor)	false
C7	CB	ALA- 128	3.53	0	Hydrophobic	false
C12	CB	ASP- 129	4.37	0	Hydrophobic	false
O14	N	ASP- 129	2.92	149.75	H-Bond (Protein Donor)	false
C10	CB	ASP- 130	3.68	0	Hydrophobic	false
C8	CG1	VAL- 132	3.64	0	Hydrophobic	false
C9	CD1	ILE- 147	4.04	0	Hydrophobic	false
C47	CG1	ILE- 150	3.47	0	Hydrophobic	false
C30	CB	PRO- 181	3.48	0	Hydrophobic	false
BR	CG1	VAL- 182	3.6	0	Hydrophobic	false
C32	CG2	VAL- 182	3.52	0	Hydrophobic	false
C33	CD1	ILE- 184	3.99	0	Hydrophobic	false
C8	CG2	ILE- 184	3.93	0	Hydrophobic	false