scPDB - 2q3k entry

Protein Data Bank Entry:

PDB ID : 2q3k

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2007-05-30

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

Chains:

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

Ligand binding site composition:

B-Factor:	26.477
Number of residues:	42
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.950	796.500

% Hydrophobic	% Polar
42.37	57.63
According to VolSite

Ligand :

HET Code:	MUW
Formula:	C34H47N4O6S
Molecular weight:	639.825 g/mol
DrugBank ID:	-
Buried Surface Area:	59.48 %
Polar Surface area:	161.05 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	4
Rings:	3
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	18

Mass center Coordinates

X	Y	Z
20.353	32.8888	14.8085

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
C13	CD2	LEU- 23	3.9	0	Hydrophobic	false
C32	CD2	LEU- 23	3.94	0	Hydrophobic	false
O23	OD1	ASP- 25	2.93	165.28	H-Bond (Ligand Donor)	false
C5	CB	ALA- 28	3.67	0	Hydrophobic	false
O40	N	ASP- 29	2.9	168.47	H-Bond (Protein Donor)	false
N38	OD2	ASP- 29	2.85	163.51	H-Bond (Ligand Donor)	false
N45	OD2	ASP- 30	2.8	156.68	H-Bond (Ligand Donor)	false
N45	OD2	ASP- 30	2.8	0	Ionic (Ligand Cationic)	false
N21	O	GLY- 48	2.77	162.78	H-Bond (Ligand Donor)	false
O43	N	GLY- 48	3.13	150.12	H-Bond (Protein Donor)	false
O9	N	ILE- 50	2.92	136.68	H-Bond (Protein Donor)	false
O8	N	ILE- 50	3.08	156.43	H-Bond (Protein Donor)	false
C14	CD1	ILE- 50	3.42	0	Hydrophobic	false
C19	CD1	ILE- 50	4.19	0	Hydrophobic	false
C5	CD1	ILE- 50	3.36	0	Hydrophobic	false
C26	CB	PRO- 81	3.6	0	Hydrophobic	false
C35	CG	PRO- 81	3.7	0	Hydrophobic	false
C13	CG1	VAL- 82	3.63	0	Hydrophobic	false
C14	CG1	VAL- 82	4.4	0	Hydrophobic	false
C29	CG1	VAL- 82	4.03	0	Hydrophobic	false
C28	CB	VAL- 82	3.87	0	Hydrophobic	false
C34	CG1	VAL- 82	4.28	0	Hydrophobic	false
C6	CD1	ILE- 84	4.24	0	Hydrophobic	false
C18	CD1	ILE- 84	3.62	0	Hydrophobic	false
C34	CD1	ILE- 84	3.69	0	Hydrophobic	false
C12	CG2	ILE- 84	4.05	0	Hydrophobic	false
N45	O	HOH- 542	3.1	150.47	H-Bond (Ligand Donor)	false