scPDB - 2r3w entry

Protein Data Bank Entry:

PDB ID : 2r3w

Resolution :1.920 Å

Experimental Method : X-ray

Deposition Date : 2007-08-30

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_HV1B5
AC:	P04587
Organism:	Human immunodeficiency virus type 1 group M subtype B
Reign:	Viruses
TaxID:	11682
EC Number:	3.4.23.16

Chains:

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

Ligand binding site composition:

B-Factor:	24.171
Number of residues:	45
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.660	722.250

% Hydrophobic	% Polar
40.19	59.81
According to VolSite

Ligand :

HET Code:	G3G
Formula:	C30H34N5O4S2
Molecular weight:	592.752 g/mol
DrugBank ID:	-
Buried Surface Area:	73 %
Polar Surface area:	160.16 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	3
Rings:	5
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
-11.8618	-20.0602	17.6801

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
C38	CD2	LEU- 23	3.59	0	Hydrophobic	false
C30	CD2	LEU- 23	3.96	0	Hydrophobic	false
N22	OD2	ASP- 25	2.69	155.57	H-Bond (Ligand Donor)	false
N22	OD1	ASP- 25	2.96	145.21	H-Bond (Ligand Donor)	false
N22	OD2	ASP- 25	2.98	125.11	H-Bond (Ligand Donor)	false
N22	OD2	ASP- 25	2.69	0	Ionic (Ligand Cationic)	false
N22	OD1	ASP- 25	2.89	0	Ionic (Ligand Cationic)	false
N22	OD1	ASP- 25	2.96	0	Ionic (Ligand Cationic)	false
N22	OD2	ASP- 25	2.98	0	Ionic (Ligand Cationic)	false
C17	CB	ALA- 28	3.76	0	Hydrophobic	false
C2	CB	ALA- 28	3.67	0	Hydrophobic	false
C1	CB	ASP- 30	4.43	0	Hydrophobic	false
N42	OD2	ASP- 30	2.67	142.72	H-Bond (Ligand Donor)	false
N43	O	ASP- 30	3.08	152.44	H-Bond (Ligand Donor)	false
C17	CG2	VAL- 32	3.77	0	Hydrophobic	false
C2	CG2	VAL- 32	3.52	0	Hydrophobic	false
C4	CG2	ILE- 47	4.32	0	Hydrophobic	false
C3	CB	ILE- 47	4.31	0	Hydrophobic	false
C6	CD1	ILE- 47	4.14	0	Hydrophobic	false
C1	CD1	ILE- 47	4.26	0	Hydrophobic	false
O40	N	ILE- 50	3.22	153.85	H-Bond (Protein Donor)	false
C26	CD1	ILE- 50	4.21	0	Hydrophobic	false
C27	CD1	ILE- 50	3.66	0	Hydrophobic	false
C18	CD1	ILE- 50	3.45	0	Hydrophobic	false
C35	CG	PRO- 81	3.54	0	Hydrophobic	false
C39	CG1	VAL- 82	3.84	0	Hydrophobic	false
C14	CG1	VAL- 82	3.69	0	Hydrophobic	false
C2	CG2	VAL- 84	3.7	0	Hydrophobic	false
C38	CG1	VAL- 84	3.98	0	Hydrophobic	false
C14	CG1	VAL- 84	3.83	0	Hydrophobic	false