scPDB - 3d1y entry

Protein Data Bank Entry:

PDB ID : 3d1y

Resolution :1.050 Å

Experimental Method : X-ray

Deposition Date : 2008-05-06

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_HV1B5
AC:	P04587
Organism:	Human immunodeficiency virus type 1 group M subtype B
Reign:	Viruses
TaxID:	11682
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:	14.824
Number of residues:	43
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.224	924.750

% Hydrophobic	% Polar
44.53	55.47
According to VolSite

Ligand :

HET Code:	ROC
Formula:	C38H51N6O5
Molecular weight:	671.849 g/mol
DrugBank ID:	DB01232
Buried Surface Area:	67.95 %
Polar Surface area:	167.94 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	6
Rings:	5
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
18.4568	23.4491	18.1843

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
C7A	CD2	LEU- 23	4.38	0	Hydrophobic	false
O2	OD1	ASP- 25	2.51	160.59	H-Bond (Protein Donor)	false
N2	O	GLY- 27	3.16	162.61	H-Bond (Ligand Donor)	false
CB	CB	ALA- 28	4.34	0	Hydrophobic	false
O	N	ASP- 29	2.97	165.33	H-Bond (Protein Donor)	false
OD1	N	ASP- 30	3	156.88	H-Bond (Protein Donor)	false
ND2	OD2	ASP- 30	3.14	156.48	H-Bond (Ligand Donor)	false
N	O	GLY- 48	3	138.24	H-Bond (Ligand Donor)	false
CD1	CG1	ILE- 50	3.87	0	Hydrophobic	false
CE1	CD1	ILE- 50	4.02	0	Hydrophobic	false
C11	CB	ILE- 50	3.96	0	Hydrophobic	false
C32	CG1	ILE- 50	4.09	0	Hydrophobic	false
C51	CG	PRO- 81	3.63	0	Hydrophobic	false
C41	CG2	VAL- 82	3.86	0	Hydrophobic	false
CB	CD1	ILE- 84	4.35	0	Hydrophobic	false
C7A	CG2	ILE- 84	3.99	0	Hydrophobic	false
CD2	CD2	LEU- 123	3.79	0	Hydrophobic	false
O2	OD2	ASP- 125	2.57	155.47	H-Bond (Ligand Donor)	false
C22	CB	ALA- 128	4.16	0	Hydrophobic	false
C32	CB	ALA- 128	4.14	0	Hydrophobic	false
C22	CB	ASP- 130	4.22	0	Hydrophobic	false
C22	CG2	VAL- 132	4.23	0	Hydrophobic	false
C32	CG2	VAL- 132	4.1	0	Hydrophobic	false
C11	CD1	ILE- 147	3.88	0	Hydrophobic	false
CB	CD1	ILE- 150	4.01	0	Hydrophobic	false
C61	CB	ILE- 150	3.98	0	Hydrophobic	false
C4A	CG	PRO- 181	4.48	0	Hydrophobic	false
C6	CB	PRO- 181	3.56	0	Hydrophobic	false
C7	CG	PRO- 181	3.8	0	Hydrophobic	false
CZ	CG	PRO- 181	3.98	0	Hydrophobic	false
C4	CG2	VAL- 182	4.11	0	Hydrophobic	false
CE2	CB	VAL- 182	4.06	0	Hydrophobic	false
C32	CD1	ILE- 184	3.83	0	Hydrophobic	false
CD1	CD1	ILE- 184	3.42	0	Hydrophobic	false