scPDB - 1eby entry

Protein Data Bank Entry:

PDB ID : 1eby

Resolution :2.290 Å

Experimental Method : X-ray

Deposition Date : 2000-01-25

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
A	50 %
B	50 %

Ligand binding site composition:

B-Factor:	13.568
Number of residues:	45
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.053	769.500

% Hydrophobic	% Polar
48.25	51.75
According to VolSite

Ligand :

HET Code:	BEB
Formula:	C38H40N2O8
Molecular weight:	652.733 g/mol
DrugBank ID:	-
Buried Surface Area:	71.44 %
Polar Surface area:	157.57 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	6
Rings:	6
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
13.1953	23.039	5.55525

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
C38	CD2	LEU- 23	3.78	0	Hydrophobic	false
C32	CD2	LEU- 23	4.39	0	Hydrophobic	false
O6	OD1	ASP- 25	2.64	129.3	H-Bond (Ligand Donor)	false
O6	OD2	ASP- 25	2.85	155.86	H-Bond (Ligand Donor)	false
N1	O	GLY- 27	3.13	165.2	H-Bond (Ligand Donor)	false
C43	CB	ALA- 28	3.59	0	Hydrophobic	false
O50	OD2	ASP- 29	3.09	170.05	H-Bond (Ligand Donor)	false
O50	N	ASP- 29	3.02	158.61	H-Bond (Protein Donor)	false
C48	CB	ASP- 29	4.41	0	Hydrophobic	false
C46	CB	ASP- 30	3.92	0	Hydrophobic	false
C44	CG1	VAL- 32	3.81	0	Hydrophobic	false
C47	CB	ILE- 47	4.41	0	Hydrophobic	false
C46	CG2	ILE- 47	4.03	0	Hydrophobic	false
C45	CD1	ILE- 47	3.8	0	Hydrophobic	false
C28	CD1	ILE- 50	3.73	0	Hydrophobic	false
C35	CB	PRO- 81	3.94	0	Hydrophobic	false
C33	CG1	VAL- 82	3.65	0	Hydrophobic	false
C33	CG1	VAL- 82	3.65	0	Hydrophobic	false
C32	CD1	ILE- 84	3.34	0	Hydrophobic	false
C24	CD2	LEU- 123	3.8	0	Hydrophobic	false
O8	OD2	ASP- 125	2.71	159.98	H-Bond (Ligand Donor)	false
N12	O	GLY- 127	3.21	169.28	H-Bond (Ligand Donor)	false
O60	O	GLY- 127	3.4	154.02	H-Bond (Ligand Donor)	false
C54	CB	ALA- 128	3.61	0	Hydrophobic	false
O60	N	ASP- 129	3.07	154.22	H-Bond (Protein Donor)	false
C58	CB	ASP- 129	4.21	0	Hydrophobic	false
C56	CB	ASP- 130	3.71	0	Hydrophobic	false
C55	CG2	VAL- 132	3.32	0	Hydrophobic	false
C56	CG2	ILE- 147	3.93	0	Hydrophobic	false
C57	CB	ILE- 147	4.25	0	Hydrophobic	false
C55	CD1	ILE- 147	3.89	0	Hydrophobic	false
C34	CD1	ILE- 150	4.43	0	Hydrophobic	false
C43	CG1	ILE- 150	4.23	0	Hydrophobic	false
C28	CG	PRO- 181	4.37	0	Hydrophobic	false
C27	CB	PRO- 181	3.7	0	Hydrophobic	false
C23	CG2	VAL- 182	3.72	0	Hydrophobic	false
C24	CG2	VAL- 182	3.57	0	Hydrophobic	false
C54	CG2	ILE- 184	4.47	0	Hydrophobic	false
C22	CD1	ILE- 184	3.47	0	Hydrophobic	false