scPDB - 3mec entry

Protein Data Bank Entry:

PDB ID : 3mec

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2010-03-31

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	91 %
B	9 %

Ligand binding site composition:

B-Factor:	45.387
Number of residues:	35
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.461	573.750

% Hydrophobic	% Polar
65.88	34.12
According to VolSite

Ligand :

HET Code:	65B
Formula:	C20H15BrN6O
Molecular weight:	435.277 g/mol
DrugBank ID:	DB06414
Buried Surface Area:	79.72 %
Polar Surface area:	120.64 Å2

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

Mass center Coordinates

X	Y	Z
9.5755	12.6226	16.9775

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
C6'	CG	PRO- 95	4.44	0	Hydrophobic	false
C6	CD1	LEU- 100	4.4	0	Hydrophobic	false
C6'	CD2	LEU- 100	3.93	0	Hydrophobic	false
C14	CD2	LEU- 100	3.63	0	Hydrophobic	false
C26	CD1	LEU- 100	4.03	0	Hydrophobic	false
N5	O	LYS- 101	2.68	169.11	H-Bond (Ligand Donor)	false
N16	N	LYS- 101	3.37	144.45	H-Bond (Protein Donor)	false
C23	CB	LYS- 103	4.22	0	Hydrophobic	false
C22	CG	LYS- 103	3.75	0	Hydrophobic	false
C3	CG1	VAL- 106	3.59	0	Hydrophobic	false
C25	CG2	VAL- 106	3.65	0	Hydrophobic	false
N18	OE1	GLU- 138	3.28	131.45	H-Bond (Ligand Donor)	false
BR	CG	GLU- 138	4.07	0	Hydrophobic	false
C2'	CG1	VAL- 179	4.46	0	Hydrophobic	false
C14	CG1	VAL- 179	3.62	0	Hydrophobic	false
BR	CG2	VAL- 179	3.44	0	Hydrophobic	false
C6'	CD2	TYR- 181	3.78	0	Hydrophobic	false
BR	CB	TYR- 181	4.06	0	Hydrophobic	false
C1	CB	TYR- 181	4.11	0	Hydrophobic	false
C2'	CB	TYR- 188	4.08	0	Hydrophobic	false
C3	CB	TYR- 188	3.45	0	Hydrophobic	false
C6'	CZ2	TRP- 229	3.5	0	Hydrophobic	false
C24	CB	LEU- 234	3.91	0	Hydrophobic	false
C5	CD1	LEU- 234	3.73	0	Hydrophobic	false
C25	CD1	LEU- 234	3.62	0	Hydrophobic	false