scPDB - 1odw entry

Protein Data Bank Entry:

PDB ID : 1odw

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 1996-09-16

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	49 %
B	51 %

Ligand binding site composition:

B-Factor:	22.841
Number of residues:	46
Including
Standard Amino Acids:	45
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.902	806.625

% Hydrophobic	% Polar
42.68	57.32
According to VolSite

Ligand :

HET Code:	0E8
Formula:	C30H46N3O6
Molecular weight:	544.703 g/mol
DrugBank ID:	-
Buried Surface Area:	63.01 %
Polar Surface area:	133.73 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	5
Rings:	2
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	16

Mass center Coordinates

X	Y	Z
5.19797	-1.90977	14.2425

Binding mode :

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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
CB	CD2	LEU- 23	4.15	0	Hydrophobic	false
CB1	CD2	LEU- 23	4.2	0	Hydrophobic	false
O	OD2	ASP- 25	2.67	169.88	H-Bond (Ligand Donor)	false
N1	OD2	ASP- 25	2.93	162.51	H-Bond (Ligand Donor)	false
N1	OD1	ASP- 25	3.03	134.36	H-Bond (Ligand Donor)	false
N1	OD1	ASP- 25	2.89	145.6	H-Bond (Ligand Donor)	false
N1	OD2	ASP- 25	3.18	146.77	H-Bond (Ligand Donor)	false
O3	OD2	ASP- 25	2.56	163.24	H-Bond (Ligand Donor)	false
N1	OD2	ASP- 25	2.93	0	Ionic (Ligand Cationic)	false
N1	OD1	ASP- 25	3.03	0	Ionic (Ligand Cationic)	false
N1	OD1	ASP- 25	2.89	0	Ionic (Ligand Cationic)	false
N1	OD2	ASP- 25	3.18	0	Ionic (Ligand Cationic)	false
N	O	GLY- 27	3.43	138.92	H-Bond (Ligand Donor)	false
N2	O	GLY- 27	3.45	126.49	H-Bond (Ligand Donor)	false
C1	CB	ALA- 28	3.95	0	Hydrophobic	false
C11	CB	ALA- 28	4.05	0	Hydrophobic	false
C1	CB	ASP- 30	4.26	0	Hydrophobic	false
C32	CB	ASP- 30	4.13	0	Hydrophobic	false
C1	CG2	VAL- 32	4.07	0	Hydrophobic	false
C3	CG2	VAL- 32	4.11	0	Hydrophobic	false
C32	CG2	VAL- 32	3.79	0	Hydrophobic	false
C2	CD1	ILE- 47	3.93	0	Hydrophobic	false
C22	CD1	ILE- 47	3.25	0	Hydrophobic	false
C2	CG2	ILE- 50	4.04	0	Hydrophobic	false
C11	CG1	ILE- 50	4.38	0	Hydrophobic	false
C22	CG1	ILE- 50	3.81	0	Hydrophobic	false
C3	CD1	ILE- 50	3.35	0	Hydrophobic	false
CD2	CG2	ILE- 50	3.46	0	Hydrophobic	false
CD21	CG	PRO- 81	3.78	0	Hydrophobic	false
CE2	CG	PRO- 81	3.59	0	Hydrophobic	false
CZ1	CG	PRO- 81	3.36	0	Hydrophobic	false
CD2	CG1	VAL- 82	3.98	0	Hydrophobic	false
CG1	CG2	VAL- 82	3.91	0	Hydrophobic	false
C3	CG1	ILE- 84	4.45	0	Hydrophobic	false
CD2	CD1	ILE- 84	4.43	0	Hydrophobic	false
C11	CD1	ILE- 84	3.82	0	Hydrophobic	false
CT	CD1	ILE- 84	4.34	0	Hydrophobic	false