scPDB - 1ebw entry

Protein Data Bank Entry:

PDB ID : 1ebw

Resolution :1.810 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	49 %
B	51 %

Ligand binding site composition:

B-Factor:	14.773
Number of residues:	39
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.785	783.000

% Hydrophobic	% Polar
44.83	55.17
According to VolSite

Ligand :

HET Code:	BEI
Formula:	C34H50N4O8
Molecular weight:	642.783 g/mol
DrugBank ID:	DB03908
Buried Surface Area:	69.01 %
Polar Surface area:	175.31 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	6
Rings:	2
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	19

Mass center Coordinates

X	Y	Z
13.1787	22.9215	5.55165

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
C45	CD2	LEU- 23	3.91	0	Hydrophobic	false
C30	CD2	LEU- 23	4.46	0	Hydrophobic	false
O27	OD1	ASP- 25	2.71	131.41	H-Bond (Ligand Donor)	false
O27	OD2	ASP- 25	2.89	159.34	H-Bond (Ligand Donor)	false
N18	O	GLY- 27	3.13	156.15	H-Bond (Ligand Donor)	false
C46	CB	ALA- 28	3.76	0	Hydrophobic	false
O24	N	ASP- 29	2.88	167.64	H-Bond (Protein Donor)	false
C46	CG1	VAL- 32	3.58	0	Hydrophobic	false
C21	CB	ILE- 47	3.97	0	Hydrophobic	false
N25	O	GLY- 48	2.93	168.25	H-Bond (Ligand Donor)	false
C4	CD1	ILE- 50	4.37	0	Hydrophobic	false
C12	CG1	ILE- 50	4.01	0	Hydrophobic	false
C39	CD1	ILE- 50	3.52	0	Hydrophobic	false
C42	CG	PRO- 81	3.61	0	Hydrophobic	false
C40	CG1	VAL- 82	3.71	0	Hydrophobic	false
C40	CG1	VAL- 82	3.68	0	Hydrophobic	false
C46	CD1	ILE- 84	3.69	0	Hydrophobic	false
C30	CD1	ILE- 84	3.42	0	Hydrophobic	false
C35	CD2	LEU- 123	3.75	0	Hydrophobic	false
O28	OD2	ASP- 125	2.7	160.09	H-Bond (Ligand Donor)	false
N8	O	GLY- 127	3.12	156.61	H-Bond (Ligand Donor)	false
C47	CB	ALA- 128	3.9	0	Hydrophobic	false
O14	N	ASP- 129	2.92	162.81	H-Bond (Protein Donor)	false
C47	CG2	VAL- 132	3.67	0	Hydrophobic	false
C11	CB	ILE- 147	3.88	0	Hydrophobic	false
N15	O	GLY- 148	2.96	164.16	H-Bond (Ligand Donor)	false
C41	CD1	ILE- 150	4.21	0	Hydrophobic	false
C22	CG1	ILE- 150	3.63	0	Hydrophobic	false
C38	CB	PRO- 181	3.67	0	Hydrophobic	false
C34	CG2	VAL- 182	3.72	0	Hydrophobic	false
C35	CG2	VAL- 182	3.68	0	Hydrophobic	false
C47	CD1	ILE- 184	3.92	0	Hydrophobic	false
C33	CD1	ILE- 184	3.54	0	Hydrophobic	false