scPDB - 2qi1 entry

Protein Data Bank Entry:

PDB ID : 2qi1

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2007-07-03

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:	22.157
Number of residues:	46
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.629	651.375

% Hydrophobic	% Polar
41.97	58.03
According to VolSite

Ligand :

HET Code:	MZ4
Formula:	C29H30N2O7S2
Molecular weight:	582.688 g/mol
DrugBank ID:	-
Buried Surface Area:	72.27 %
Polar Surface area:	173.02 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	4
Rings:	4
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	12

Mass center Coordinates

X	Y	Z
19.8773	30.7851	14.0263

Binding mode :

What is Poseview ?

2D View
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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
C33	CD2	LEU- 23	4.38	0	Hydrophobic	false
O18	OD2	ASP- 25	2.55	160.02	H-Bond (Protein Donor)	false
O18	OD1	ASP- 25	2.82	125.85	H-Bond (Ligand Donor)	false
O18	OD2	ASP- 25	2.76	166.07	H-Bond (Ligand Donor)	false
N20	O	GLY- 27	3.38	130.46	H-Bond (Ligand Donor)	false
C16	CB	ALA- 28	4.07	0	Hydrophobic	false
C4	CB	ALA- 28	3.46	0	Hydrophobic	false
C23	CB	ALA- 28	3.41	0	Hydrophobic	false
C2	CB	ASP- 30	3.96	0	Hydrophobic	false
C3	CG2	VAL- 32	3.54	0	Hydrophobic	false
C24	CG2	VAL- 32	4.09	0	Hydrophobic	false
C7	CB	ILE- 47	4.07	0	Hydrophobic	false
C20	CG2	ILE- 47	3.87	0	Hydrophobic	false
C2	CD1	ILE- 47	4.15	0	Hydrophobic	false
C25	CD1	ILE- 47	4.2	0	Hydrophobic	false
O29	O	GLY- 48	2.67	158.83	H-Bond (Ligand Donor)	false
C5	CD1	ILE- 50	4.4	0	Hydrophobic	false
S1	CG1	ILE- 50	4.14	0	Hydrophobic	false
C36	CB	ILE- 50	4.19	0	Hydrophobic	false
C22	CD1	ILE- 50	3.67	0	Hydrophobic	false
S1	CG	PRO- 81	3.89	0	Hydrophobic	false
C36	CG	PRO- 81	3.87	0	Hydrophobic	false
C36	CG1	VAL- 82	3.55	0	Hydrophobic	false
C4	CD1	ILE- 84	4.4	0	Hydrophobic	false
C37	CD1	ILE- 84	3.94	0	Hydrophobic	false
C23	CD1	ILE- 84	3.58	0	Hydrophobic	false