scPDB - 1ody entry

Protein Data Bank Entry:

PDB ID : 1ody

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 1998-07-13

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_HV1H2
AC:	P04585
Organism:	Human immunodeficiency virus type 1 group M subtype B
Reign:	Viruses
TaxID:	11706
EC Number:	3.4.23.16

Chains:

Chain Name:	Percentage of Residues within binding site
A	55 %
B	45 %

Ligand binding site composition:

B-Factor:	28.910
Number of residues:	44
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.946	621.000

% Hydrophobic	% Polar
44.57	55.43
According to VolSite

Ligand :

HET Code:	LP1
Formula:	C45H58N6O7
Molecular weight:	794.978 g/mol
DrugBank ID:	-
Buried Surface Area:	58.36 %
Polar Surface area:	208.81 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	7
Rings:	4
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	20

Mass center Coordinates

X	Y	Z
-9.1259	14.8115	28.0854

Binding mode :

What is Poseview ?

2D View
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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
C30	CD1	LEU- 23	4.24	0	Hydrophobic	false
C54	CD1	LEU- 23	4.46	0	Hydrophobic	false
O34	OD2	ASP- 25	2.89	134.65	H-Bond (Ligand Donor)	false
O34	OD1	ASP- 25	2.86	160.77	H-Bond (Ligand Donor)	false
N26	O	GLY- 27	2.94	141.92	H-Bond (Ligand Donor)	false
N37	O	GLY- 27	3.38	153.29	H-Bond (Ligand Donor)	false
C24	CB	ALA- 28	3.35	0	Hydrophobic	false
C39	CB	ALA- 28	4.02	0	Hydrophobic	false
N4	OD2	ASP- 29	3.11	153.13	H-Bond (Ligand Donor)	false
N58	OD2	ASP- 29	3.33	144.2	H-Bond (Ligand Donor)	false
O18	N	ASP- 29	2.77	152.39	H-Bond (Protein Donor)	false
O42	N	ASP- 29	2.82	162.47	H-Bond (Protein Donor)	false
C24	CG1	VAL- 32	4.24	0	Hydrophobic	false
C25	CG1	VAL- 32	4.43	0	Hydrophobic	false
C40	CG1	VAL- 32	4.46	0	Hydrophobic	false
C1	CG2	ILE- 47	3.28	0	Hydrophobic	false
C25	CG2	ILE- 47	4.41	0	Hydrophobic	false
N19	O	GLY- 48	2.87	170.37	H-Bond (Ligand Donor)	false
N43	O	GLY- 48	2.64	163.79	H-Bond (Ligand Donor)	false
C31	CD1	ILE- 50	3.54	0	Hydrophobic	false
C40	CD1	ILE- 50	3.92	0	Hydrophobic	false
C53	CD1	ILE- 50	3.9	0	Hydrophobic	false
C31	CG	PRO- 81	4.02	0	Hydrophobic	false
C48	CB	PRO- 81	4.06	0	Hydrophobic	false
C14	CB	PRO- 81	4.09	0	Hydrophobic	false
C49	CG	PRO- 81	3.23	0	Hydrophobic	false
C15	CG	PRO- 81	3.73	0	Hydrophobic	false
C30	CG2	VAL- 82	3.5	0	Hydrophobic	false
C53	CG2	VAL- 82	3.37	0	Hydrophobic	false
C24	CD1	ILE- 84	3.34	0	Hydrophobic	false
C28	CD1	ILE- 84	3.96	0	Hydrophobic	false
C55	CD1	ILE- 84	4.18	0	Hydrophobic	false
C31	CD1	ILE- 84	4.04	0	Hydrophobic	false