scPDB - 1ec3 entry

Protein Data Bank Entry:

PDB ID : 1ec3

Resolution :1.800 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	51 %
B	49 %

Ligand binding site composition:

B-Factor:	20.794
Number of residues:	43
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.895	810.000

% Hydrophobic	% Polar
43.75	56.25
According to VolSite

Ligand :

HET Code:	MS3
Formula:	C42H52N6O8
Molecular weight:	768.898 g/mol
DrugBank ID:	DB03803
Buried Surface Area:	59.3 %
Polar Surface area:	201.09 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	6
Rings:	4
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	21

Mass center Coordinates

X	Y	Z
12.8874	22.7179	5.84645

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
DuAr	CZ	ARG- 8	3.94	38.81	Pi/Cation	false
C31	CD2	LEU- 23	3.75	0	Hydrophobic	false
O33	OD2	ASP- 25	2.92	158.87	H-Bond (Ligand Donor)	false
N36	O	GLY- 27	3.16	162.2	H-Bond (Ligand Donor)	false
C38	CB	ALA- 28	4.04	0	Hydrophobic	false
O42	N	ASP- 29	2.86	168.32	H-Bond (Protein Donor)	false
C40	CG2	VAL- 32	4.27	0	Hydrophobic	false
C39	CB	ILE- 47	3.97	0	Hydrophobic	false
N43	O	GLY- 48	3	165.41	H-Bond (Ligand Donor)	false
C25	CG1	ILE- 50	3.68	0	Hydrophobic	false
C04	CG	PRO- 81	3.27	0	Hydrophobic	false
C01	CG1	VAL- 82	3.4	0	Hydrophobic	false
C01	CG1	VAL- 82	3.4	0	Hydrophobic	false
C40	CD1	ILE- 84	4.41	0	Hydrophobic	false
C06	CD1	ILE- 84	3.65	0	Hydrophobic	false
C12	CD2	LEU- 123	3.59	0	Hydrophobic	false
O32	OD2	ASP- 125	2.6	167.34	H-Bond (Ligand Donor)	false
O32	OD1	ASP- 125	2.86	123.88	H-Bond (Ligand Donor)	false
N21	O	GLY- 127	3.11	158.23	H-Bond (Ligand Donor)	false
C23	CB	ALA- 128	3.84	0	Hydrophobic	false
O27	N	ASP- 129	2.88	167.94	H-Bond (Protein Donor)	false
C24	CG2	VAL- 132	4.29	0	Hydrophobic	false
C25	CG2	VAL- 132	4.44	0	Hydrophobic	false
C24	CD1	ILE- 147	3.88	0	Hydrophobic	false
N28	O	GLY- 148	2.97	164.88	H-Bond (Ligand Donor)	false
C05	CD1	ILE- 150	4.23	0	Hydrophobic	false
C08	CG	PRO- 181	4.43	0	Hydrophobic	false
C09	CB	PRO- 181	3.55	0	Hydrophobic	false
C11	CG2	VAL- 182	3.58	0	Hydrophobic	false
C25	CD1	ILE- 184	4.29	0	Hydrophobic	false
C13	CD1	ILE- 184	3.34	0	Hydrophobic	false