scPDB - 1siv entry

Protein Data Bank Entry:

PDB ID : 1siv

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 1993-08-24

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_SIVM1
AC:	P05896
Organism:	Simian immunodeficiency virus
Reign:	Viruses
TaxID:	11733
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	50 %
B	50 %

Ligand binding site composition:

B-Factor:	10.638
Number of residues:	36
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.872	624.375

% Hydrophobic	% Polar
45.41	54.59
According to VolSite

Ligand :

HET Code:	PSI
Formula:	C29H48N5O7
Molecular weight:	578.721 g/mol
DrugBank ID:	DB04191
Buried Surface Area:	62.31 %
Polar Surface area:	190.56 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	6
Rings:	1
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	17

Mass center Coordinates

X	Y	Z
3.16676	11.3681	40.196

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
CD2	CD2	LEU- 23	4.33	0	Hydrophobic	false
OS	OD1	ASP- 25	2.98	131.7	H-Bond (Ligand Donor)	false
OS	OD2	ASP- 25	3.08	168.86	H-Bond (Ligand Donor)	false
N2	O	GLY- 27	3.03	154.7	H-Bond (Ligand Donor)	false
N4	O	GLY- 27	3.02	159.56	H-Bond (Ligand Donor)	false
CB1	CB	ALA- 28	4.05	0	Hydrophobic	false
CB3	CB	ALA- 28	4.18	0	Hydrophobic	false
N	OD2	ASP- 29	2.79	157.93	H-Bond (Ligand Donor)	false
N	OD2	ASP- 29	2.79	0	Ionic (Ligand Cationic)	false
O	N	ASP- 29	2.77	147.62	H-Bond (Protein Donor)	false
O3	N	ASP- 29	2.95	162.92	H-Bond (Protein Donor)	false
N	OD2	ASP- 30	2.85	157.15	H-Bond (Ligand Donor)	false
N	OD2	ASP- 30	2.85	0	Ionic (Ligand Cationic)	false
O	N	ASP- 30	3.45	159.58	H-Bond (Protein Donor)	false
CB1	CD1	ILE- 32	3.28	0	Hydrophobic	false
CG1	CD1	ILE- 32	4.05	0	Hydrophobic	false
CB1	CG1	VAL- 47	4.26	0	Hydrophobic	false
CG1	CB	VAL- 47	3.57	0	Hydrophobic	false
C6	CG1	VAL- 47	4.01	0	Hydrophobic	false
N1	O	GLY- 48	2.88	158.08	H-Bond (Ligand Donor)	false
N5	O	GLY- 48	2.91	171.47	H-Bond (Ligand Donor)	false
O4	N	GLY- 48	2.98	158.28	H-Bond (Protein Donor)	false
CB1	CG1	ILE- 50	4.42	0	Hydrophobic	false
CD1	CD1	ILE- 50	3.98	0	Hydrophobic	false
CG2	CG1	ILE- 50	4.06	0	Hydrophobic	false
CE1	CG	PRO- 81	3.66	0	Hydrophobic	false
CG21	CG1	ILE- 82	3.92	0	Hydrophobic	false
CZ	CG2	ILE- 82	3.45	0	Hydrophobic	false
CB1	CD1	ILE- 84	4.34	0	Hydrophobic	false
CG2	CD1	ILE- 84	4.11	0	Hydrophobic	false
CM	CD1	ILE- 84	3.76	0	Hydrophobic	false
CB2	CD1	ILE- 84	4	0	Hydrophobic	false