scPDB - 1yt9 entry

Protein Data Bank Entry:

PDB ID : 1yt9

Resolution :3.000 Å

Experimental Method : X-ray

Deposition Date : 2005-02-10

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:	/

Chains:

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

Ligand binding site composition:

B-Factor:	7.451
Number of residues:	44
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.134	1012.500

% Hydrophobic	% Polar
45.67	54.33
According to VolSite

Ligand :

HET Code:	OIS
Formula:	C34H46N6O6S2
Molecular weight:	698.896 g/mol
DrugBank ID:	DB04748
Buried Surface Area:	58.3 %
Polar Surface area:	192.36 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	3
Rings:	4
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	16

Mass center Coordinates

X	Y	Z
14.1271	22.3827	6.71267

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	3.97	33.12	Pi/Cation	false
C12	CD2	LEU- 23	4.02	0	Hydrophobic	false
C17	CD2	LEU- 23	4.05	0	Hydrophobic	false
O1	OD1	ASP- 25	3.11	135.61	H-Bond (Ligand Donor)	false
O1	OD2	ASP- 25	2.92	160.28	H-Bond (Ligand Donor)	false
C5	CB	ALA- 28	4.48	0	Hydrophobic	false
C37	CB	ALA- 28	3.91	0	Hydrophobic	false
C21	CB	ALA- 28	3.88	0	Hydrophobic	false
O5	N	ASP- 29	2.67	139.14	H-Bond (Protein Donor)	false
C35	CB	ASP- 29	3.91	0	Hydrophobic	false
C36	CG1	VAL- 32	3.85	0	Hydrophobic	false
C22	CG2	VAL- 32	3.58	0	Hydrophobic	false
C34	CG2	ILE- 47	3.92	0	Hydrophobic	false
C23	CD1	ILE- 47	3.77	0	Hydrophobic	false
C18	CG1	ILE- 50	3.93	0	Hydrophobic	false
C22	CG1	ILE- 50	3.7	0	Hydrophobic	false
C15	CG	PRO- 81	3.43	0	Hydrophobic	false
C17	CG2	VAL- 82	3.99	0	Hydrophobic	false
S2	CB	VAL- 82	4.36	0	Hydrophobic	false
C13	CG1	VAL- 82	3.36	0	Hydrophobic	false
C4	CD1	ILE- 84	3.91	0	Hydrophobic	false
C17	CD1	ILE- 84	3.68	0	Hydrophobic	false