scPDB - 3dmj entry

Protein Data Bank Entry:

PDB ID : 3dmj

Resolution :2.600 Å

Experimental Method : X-ray

Deposition Date : 2008-07-01

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Pol protein
ID:	A7YKL0_9HIV1
AC:	A7YKL0
Organism:	Human immunodeficiency virus 1
Reign:	Viruses
TaxID:	11676
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	94 %
B	6 %

Ligand binding site composition:

B-Factor:	52.017
Number of residues:	36
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.744	536.625

% Hydrophobic	% Polar
68.55	31.45
According to VolSite

Ligand :

HET Code:	GWE
Formula:	C23H19ClF4N2O5S
Molecular weight:	546.919 g/mol
DrugBank ID:	-
Buried Surface Area:	72.61 %
Polar Surface area:	121.88 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	4
Rings:	3
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-3.76419	-34.4575	24.3173

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
F2	CG	PRO- 95	3.39	0	Hydrophobic	false
C2	CD1	LEU- 100	4.29	0	Hydrophobic	false
C8	CD1	LEU- 100	3.93	0	Hydrophobic	false
C15	CB	LEU- 100	3.84	0	Hydrophobic	false
C1	CB	LEU- 100	3.91	0	Hydrophobic	false
F2	CD2	LEU- 100	3.45	0	Hydrophobic	false
O3	N	LYS- 103	2.86	165.05	H-Bond (Protein Donor)	false
C5	CG	LYS- 103	3.91	0	Hydrophobic	false
N2	O	LYS- 104	3.39	176.51	H-Bond (Ligand Donor)	false
O4	N	ALA- 106	3.29	165.07	H-Bond (Protein Donor)	false
C3	CB	ALA- 106	3.97	0	Hydrophobic	false
C22	CB	ALA- 106	3.72	0	Hydrophobic	false
CL1	CG2	VAL- 179	3.74	0	Hydrophobic	false
F3	CB	CYS- 181	3.32	0	Hydrophobic	false
CL1	SG	CYS- 181	3.84	0	Hydrophobic	false
F1	CB	TYR- 183	4.22	0	Hydrophobic	false
C3	CB	TYR- 188	3.92	0	Hydrophobic	false
CL1	CB	TYR- 188	4.05	0	Hydrophobic	false
F1	CE1	TYR- 188	3.31	0	Hydrophobic	false
F4	CE2	TYR- 188	3.62	0	Hydrophobic	false
C11	CE2	TYR- 188	3.47	0	Hydrophobic	false
C13	CB	TYR- 188	4.11	0	Hydrophobic	false
F3	CD1	TYR- 188	3.45	0	Hydrophobic	false
C19	CG	PRO- 225	4.15	0	Hydrophobic	false
C23	CD2	PHE- 227	3.8	0	Hydrophobic	false
F4	CB	PHE- 227	3.45	0	Hydrophobic	false
C14	CZ2	TRP- 229	4.16	0	Hydrophobic	false
F1	CH2	TRP- 229	3.29	0	Hydrophobic	false
F2	CE2	TRP- 229	3.94	0	Hydrophobic	false
F4	CE3	TRP- 229	3.76	0	Hydrophobic	false
C23	CB	LEU- 234	4.01	0	Hydrophobic	false
C9	CD1	LEU- 234	3.38	0	Hydrophobic	false
C19	CG	PRO- 236	3.99	0	Hydrophobic	false
C20	CB	PRO- 236	4.05	0	Hydrophobic	false
C15	CD1	TYR- 318	3.6	0	Hydrophobic	false