scPDB - 3qrm entry

Protein Data Bank Entry:

PDB ID : 3qrm

Resolution :1.730 Å

Experimental Method : X-ray

Deposition Date : 2011-02-18

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_HV1BR
AC:	P03367
Organism:	Human immunodeficiency virus type 1 group M subtype B
Reign:	Viruses
TaxID:	11686
EC Number:	3.4.23.16

Chains:

Chain Name:	Percentage of Residues within binding site
A	47 %
B	53 %

Ligand binding site composition:

B-Factor:	12.886
Number of residues:	44
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.810	799.875

% Hydrophobic	% Polar
43.04	56.96
According to VolSite

Ligand :

HET Code:	NK7
Formula:	C27H27F6N4O3S
Molecular weight:	601.584 g/mol
DrugBank ID:	-
Buried Surface Area:	71.03 %
Polar Surface area:	117.48 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	3
Rings:	4
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
18.3153	19.6147	4.96895

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
C25	CD2	LEU- 23	3.74	0	Hydrophobic	false
N4	OD1	ASP- 25	3.07	0	Ionic (Ligand Cationic)	false
N4	OD1	ASP- 25	2.74	0	Ionic (Ligand Cationic)	false
N4	OD2	ASP- 25	2.86	0	Ionic (Ligand Cationic)	false
N4	OD2	ASP- 25	2.97	0	Ionic (Ligand Cationic)	false
N4	OD1	ASP- 25	2.74	145.58	H-Bond (Ligand Donor)	false
N4	OD2	ASP- 25	2.86	144.7	H-Bond (Ligand Donor)	false
N4	OD2	ASP- 25	2.97	143.23	H-Bond (Ligand Donor)	false
C9	CB	ALA- 28	3.67	0	Hydrophobic	false
C32	CB	ALA- 28	3.88	0	Hydrophobic	false
F39	CB	ASP- 29	3.42	0	Hydrophobic	false
N36	OD1	ASP- 30	3.17	163.04	H-Bond (Ligand Donor)	false
O37	N	ASP- 30	3.09	143.43	H-Bond (Protein Donor)	false
F40	CB	ASP- 30	3.31	0	Hydrophobic	false
C32	CG2	VAL- 32	4.11	0	Hydrophobic	false
F40	CG2	VAL- 32	4.2	0	Hydrophobic	false
C10	CG2	VAL- 32	3.7	0	Hydrophobic	false
C12	CB	ILE- 47	4.32	0	Hydrophobic	false
C11	CD1	ILE- 47	4.33	0	Hydrophobic	false
F40	CG2	ILE- 47	3.23	0	Hydrophobic	false
C13	CG2	ILE- 50	4.35	0	Hydrophobic	false
C30	CB	ILE- 50	4.32	0	Hydrophobic	false
C7	CB	ILE- 50	3.91	0	Hydrophobic	false
C31	CD1	ILE- 50	3.64	0	Hydrophobic	false
O28	N	ILE- 50	2.97	166.73	H-Bond (Protein Donor)	false
O29	N	ILE- 50	3.29	148.05	H-Bond (Protein Donor)	false
F40	CD1	LEU- 76	3.64	0	Hydrophobic	false
F18	CB	PRO- 81	3.63	0	Hydrophobic	false
C15	CG	PRO- 81	3.67	0	Hydrophobic	false
F20	CG1	VAL- 82	4.08	0	Hydrophobic	false
C24	CG1	VAL- 82	3.63	0	Hydrophobic	false
C7	CD1	ILE- 84	3.92	0	Hydrophobic	false
C9	CD1	ILE- 84	4.17	0	Hydrophobic	false
C25	CD1	ILE- 84	3.79	0	Hydrophobic	false