scPDB - 1ebk entry

Protein Data Bank Entry:

PDB ID : 1ebk

Resolution :2.060 Å

Experimental Method : X-ray

Deposition Date : 2000-01-24

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_HV1B1
AC:	P03366
Organism:	Human immunodeficiency virus type 1 group M subtype B
Reign:	Viruses
TaxID:	11678
EC Number:	3.4.23.16

Chains:

Chain Name:	Percentage of Residues within binding site
E	54 %
F	46 %

Ligand binding site composition:

B-Factor:	12.157
Number of residues:	49
Including
Standard Amino Acids:	48
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.235	769.500

% Hydrophobic	% Polar
49.12	50.88
According to VolSite

Ligand :

HET Code:	0Q4
Formula:	C40H71N11O8
Molecular weight:	834.061 g/mol
DrugBank ID:	-
Buried Surface Area:	54.11 %
Polar Surface area:	336.61 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	11
Rings:	1
Aromatic rings:	1
Anionic atoms:	1
Cationic atoms:	3
Rule of Five Violation:	3
Rotatable Bonds:	30

Mass center Coordinates

X	Y	Z
-2.76702	4.03939	7.43876

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
CB2	CD2	LEU- 23	4.36	0	Hydrophobic	false
CD2	CD2	LEU- 23	4.43	0	Hydrophobic	false
CG5	CB	ALA- 28	3.89	0	Hydrophobic	false
O3	N	ASP- 29	2.61	153.47	H-Bond (Protein Donor)	false
CG5	CB	ASP- 30	3.93	0	Hydrophobic	false
O5	NZ	LYS- 45	2.73	143.98	H-Bond (Protein Donor)	false
N5	O	GLY- 48	3.09	159.83	H-Bond (Ligand Donor)	false
O4	N	GLY- 48	2.77	150.81	H-Bond (Protein Donor)	false
CG1	CG1	ILE- 50	3.65	0	Hydrophobic	false
CG6	CE2	PHE- 53	4.05	0	Hydrophobic	false
CD1	CG	PRO- 81	3.94	0	Hydrophobic	false
CG3	CG1	VAL- 82	3.74	0	Hydrophobic	false
CB2	CD1	ILE- 84	3.77	0	Hydrophobic	false
CE1	CD2	LEU- 123	3.21	0	Hydrophobic	false
N2	O	GLY- 127	3.07	129.3	H-Bond (Ligand Donor)	false
CG1	CB	ALA- 128	3.43	0	Hydrophobic	false
O	N	ASP- 129	2.79	169.27	H-Bond (Protein Donor)	false
CG1	CG1	VAL- 132	4.37	0	Hydrophobic	false
CB	CB	ILE- 147	4.43	0	Hydrophobic	false
CD	CG2	ILE- 147	3.98	0	Hydrophobic	false
CG2	CD1	ILE- 147	3.88	0	Hydrophobic	false
N1	O	GLY- 148	2.93	158.89	H-Bond (Ligand Donor)	false
CB4	CD1	ILE- 150	4.16	0	Hydrophobic	false
CE2	CG	PRO- 181	4.02	0	Hydrophobic	false
CE2	CB	VAL- 182	3.81	0	Hydrophobic	false
CZ1	CG2	VAL- 182	3.49	0	Hydrophobic	false
CB1	CD1	ILE- 184	4.47	0	Hydrophobic	false
CG1	CG1	ILE- 184	4.28	0	Hydrophobic	false