scPDB - 2rkg entry

Protein Data Bank Entry:

PDB ID : 2rkg

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2007-10-16

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:	A0F6C5_9HIV1
AC:	A0F6C5
Organism:	Human immunodeficiency virus 1
Reign:	Viruses
TaxID:	11676
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	51 %
B	49 %

Ligand binding site composition:

B-Factor:	33.702
Number of residues:	42
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.420	398.250

% Hydrophobic	% Polar
44.07	55.93
According to VolSite

Ligand :

HET Code:	AB1
Formula:	C37H48N4O5
Molecular weight:	628.801 g/mol
DrugBank ID:	DB01601
Buried Surface Area:	60.69 %
Polar Surface area:	120 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	4
Rings:	4
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	15

Mass center Coordinates

X	Y	Z
-9.56354	15.315	0.386304

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
C22	CD2	LEU- 23	4.36	0	Hydrophobic	false
C5	CD2	LEU- 23	3.9	0	Hydrophobic	false
O4	OD2	ASP- 25	2.62	148.5	H-Bond (Protein Donor)	false
O4	OD1	ASP- 25	2.87	147.88	H-Bond (Ligand Donor)	false
O4	OD2	ASP- 25	2.8	136.95	H-Bond (Ligand Donor)	false
N3	O	GLY- 27	3.06	165.44	H-Bond (Ligand Donor)	false
C28	CB	ALA- 28	3.93	0	Hydrophobic	false
C15	CB	ALA- 28	3.66	0	Hydrophobic	false
O1	N	ASP- 29	2.66	149.99	H-Bond (Protein Donor)	false
C33	CB	ASP- 29	3.68	0	Hydrophobic	false
C15	CB	ASP- 30	4.25	0	Hydrophobic	false
C31	CB	ASP- 30	3.53	0	Hydrophobic	false
C36	CG2	ILE- 32	3.85	0	Hydrophobic	false
C37	CG1	VAL- 48	4.17	0	Hydrophobic	false
C13	CG1	VAL- 48	4.25	0	Hydrophobic	false
C30	CG1	VAL- 48	3.91	0	Hydrophobic	false
C31	CG1	VAL- 48	3.81	0	Hydrophobic	false
C27	CD1	ILE- 51	3.92	0	Hydrophobic	false
C36	CD1	ILE- 51	4.08	0	Hydrophobic	false
C9	CG1	ILE- 51	3.96	0	Hydrophobic	false
C14	CD1	ILE- 51	3.7	0	Hydrophobic	false
C17	CB	PRO- 82	3.88	0	Hydrophobic	false
C7	CG	PRO- 82	4.3	0	Hydrophobic	false
C16	CG	PRO- 82	3.47	0	Hydrophobic	false
C14	CD1	ILE- 85	3.76	0	Hydrophobic	false
C22	CD1	ILE- 85	3.9	0	Hydrophobic	false
C23	CD1	ILE- 85	4.5	0	Hydrophobic	false
C4	CD1	ILE- 85	3.76	0	Hydrophobic	false
O2	O	HOH- 1006	2.71	179.97	H-Bond (Protein Donor)	false