scPDB - 1a8g entry

Protein Data Bank Entry:

PDB ID : 1a8g

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 1998-03-24

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_HV1BR
AC:	P03367
Organism:	Human immunodeficiency virus type 1 group M subtype B
Reign:	Viruses
TaxID:	11686
EC Number:	3.4.23.16

Chains:

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

Ligand binding site composition:

B-Factor:	17.082
Number of residues:	44
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.834	729.000

% Hydrophobic	% Polar
43.06	56.94
According to VolSite

Ligand :

HET Code:	2Z4
Formula:	C46H60N5O9
Molecular weight:	826.997 g/mol
DrugBank ID:	-
Buried Surface Area:	62.34 %
Polar Surface area:	201.15 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	7
Rings:	4
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	22

Mass center Coordinates

X	Y	Z
-9.364	15.2765	28.0859

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
CD3	CD1	LEU- 23	4.12	0	Hydrophobic	false
OH	OD2	ASP- 25	2.66	153.37	H-Bond (Protein Donor)	false
OH	OD1	ASP- 25	3.27	168.65	H-Bond (Ligand Donor)	false
OH	OD2	ASP- 25	3.37	132.81	H-Bond (Ligand Donor)	false
N2	OD2	ASP- 25	3.42	124.77	H-Bond (Ligand Donor)	false
N1	O	GLY- 27	2.93	150.36	H-Bond (Ligand Donor)	false
N3	O	GLY- 27	3.19	164.97	H-Bond (Ligand Donor)	false
CB3	CB	ALA- 28	3.96	0	Hydrophobic	false
CG1	CB	ALA- 28	4.02	0	Hydrophobic	false
O1	N	ASP- 29	3.15	178.04	H-Bond (Protein Donor)	false
O4	N	ASP- 29	2.89	166.26	H-Bond (Protein Donor)	false
CG2	CB	ASP- 30	3.9	0	Hydrophobic	false
CG12	CB	ASP- 30	4.21	0	Hydrophobic	false
OH1	OD2	ASP- 30	2.91	153.93	H-Bond (Ligand Donor)	false
CG1	CG1	VAL- 32	4.15	0	Hydrophobic	false
CG22	CG1	VAL- 32	4.23	0	Hydrophobic	false
CG3	CD1	ILE- 47	3.58	0	Hydrophobic	false
CG12	CD1	ILE- 47	4.17	0	Hydrophobic	false
C3	CB	ILE- 47	4.09	0	Hydrophobic	false
C7	CG2	ILE- 47	3.56	0	Hydrophobic	false
CE11	CG2	ILE- 47	3.54	0	Hydrophobic	false
N	O	GLY- 48	2.94	148.48	H-Bond (Ligand Donor)	false
N4	O	GLY- 48	2.8	140.06	H-Bond (Ligand Donor)	false
CG3	CG1	ILE- 50	3.98	0	Hydrophobic	false
CD1	CG2	ILE- 50	4.03	0	Hydrophobic	false
CD4	CG2	ILE- 50	3.56	0	Hydrophobic	false
CM2	CB	PRO- 81	4.34	0	Hydrophobic	false
CE1	CG	PRO- 81	3.71	0	Hydrophobic	false
CE3	CG	PRO- 81	3.99	0	Hydrophobic	false
CM2	CG1	VAL- 82	4.46	0	Hydrophobic	false
CE2	CG2	VAL- 82	3.42	0	Hydrophobic	false
CD3	CG2	VAL- 82	3.5	0	Hydrophobic	false
CG1	CG2	ILE- 84	4	0	Hydrophobic	false
CG22	CG2	ILE- 84	4.11	0	Hydrophobic	false
CB1	CD1	ILE- 84	3.87	0	Hydrophobic	false
CG21	CD1	ILE- 84	3.9	0	Hydrophobic	false
O1	O	HOH- 127	3.48	123.29	H-Bond (Protein Donor)	false