scPDB - 4mfb entry

Protein Data Bank Entry:

PDB ID : 4mfb

Resolution :2.880 Å

Experimental Method : X-ray

Deposition Date : 2013-08-27

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_HV1B1
AC:	P03366
Organism:	Human immunodeficiency virus type 1 group M subtype B
Reign:	Viruses
TaxID:	11678
EC Number:	2.7.7.49

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	56.811
Number of residues:	32
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.225	745.875

% Hydrophobic	% Polar
66.06	33.94
According to VolSite

Ligand :

HET Code:	29T
Formula:	C21H16N4O4
Molecular weight:	388.376 g/mol
DrugBank ID:	-
Buried Surface Area:	75.75 %
Polar Surface area:	96.07 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	1
Rings:	4
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
494.282	-25.7717	23.7567

Binding mode :

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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
C0D	CB	LEU- 100	3.72	0	Hydrophobic	false
O0Q	N	LYS- 103	3.06	166.54	H-Bond (Protein Donor)	false
C00	CG	LYS- 103	4.16	0	Hydrophobic	false
C05	CG2	VAL- 106	3.78	0	Hydrophobic	false
C04	CG1	VAL- 106	3.55	0	Hydrophobic	false
C01	CG1	VAL- 179	4.16	0	Hydrophobic	false
C02	CD2	TYR- 181	3.39	0	Hydrophobic	false
DuAr	DuAr	TYR- 188	3.44	0	Aromatic Face/Face	false
C03	CB	TYR- 188	3.36	0	Hydrophobic	false
C0E	CE1	TYR- 318	3.56	0	Hydrophobic	false