scPDB - 3m8q entry

Protein Data Bank Entry:

PDB ID : 3m8q

Resolution :2.700 Å

Experimental Method : X-ray

Deposition Date : 2010-03-18

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_HV1H2
AC:	P04585
Organism:	Human immunodeficiency virus type 1 group M subtype B
Reign:	Viruses
TaxID:	11706
EC Number:	2.7.7.49

Chains:

Chain Name:	Percentage of Residues within binding site
A	97 %
B	3 %

Ligand binding site composition:

B-Factor:	73.406
Number of residues:	35
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.766	712.125

% Hydrophobic	% Polar
65.40	34.60
According to VolSite

Ligand :

HET Code:	DJZ
Formula:	C26H30N5O3S
Molecular weight:	492.613 g/mol
DrugBank ID:	-
Buried Surface Area:	71.13 %
Polar Surface area:	117.78 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	2
Rings:	4
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
50.8569	65.9604	16.1972

Binding mode :

What is Poseview ?

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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
C14	CG	PRO- 95	4.47	0	Hydrophobic	false
C7	CD2	LEU- 100	3.88	0	Hydrophobic	false
C14	CD2	LEU- 100	4.06	0	Hydrophobic	false
C19	CB	LEU- 100	3.72	0	Hydrophobic	false
N17	O	LYS- 101	2.75	156.46	H-Bond (Ligand Donor)	false
C23	CG	LYS- 103	3.78	0	Hydrophobic	false
C10	CG1	VAL- 106	4.36	0	Hydrophobic	false
C23	CG2	VAL- 106	3.9	0	Hydrophobic	false
C29	CB	VAL- 106	4.01	0	Hydrophobic	false
C31	CG2	VAL- 106	3.59	0	Hydrophobic	false
O34	N	VAL- 106	2.84	140.92	H-Bond (Protein Donor)	false
C7	CG	GLU- 138	4.35	0	Hydrophobic	false
C7	CG1	VAL- 179	3.57	0	Hydrophobic	false
C15	CG1	VAL- 179	3.86	0	Hydrophobic	false
C14	CD2	TYR- 181	3.54	0	Hydrophobic	false
C8	CB	TYR- 181	3.77	0	Hydrophobic	false
C15	CB	TYR- 188	4.01	0	Hydrophobic	false
C10	CB	TYR- 188	3.47	0	Hydrophobic	false
C35	CE2	PHE- 227	3.49	0	Hydrophobic	false
C14	CZ2	TRP- 229	3.57	0	Hydrophobic	false
C11	CD2	LEU- 234	4	0	Hydrophobic	false
C28	CG	PRO- 236	4.27	0	Hydrophobic	false
C19	CE2	TYR- 318	3.95	0	Hydrophobic	false
N21	O	HOH- 567	2.78	138.38	H-Bond (Ligand Donor)	false