scPDB - 1jld entry

Protein Data Bank Entry:

PDB ID : 1jld

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 1997-05-31

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_HV2RO
AC:	P04584
Organism:	Human immunodeficiency virus type 2 subtype A
Reign:	Viruses
TaxID:	11720
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	14.566
Number of residues:	42
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.070	810.000

% Hydrophobic	% Polar
43.75	56.25
According to VolSite

Ligand :

HET Code:	0PP
Formula:	C37H51N5O6
Molecular weight:	661.831 g/mol
DrugBank ID:	-
Buried Surface Area:	63.07 %
Polar Surface area:	169.74 Å2

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

Mass center Coordinates

X	Y	Z
51.0216	23.0064	4.27435

Binding mode :

What is Poseview ?

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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
CT3	CD1	LEU- 23	4.3	0	Hydrophobic	false
CT4	CD1	LEU- 23	3.76	0	Hydrophobic	false
CD2	CD2	LEU- 23	3.78	0	Hydrophobic	false
OXT	OD2	ASP- 25	3.08	157.51	H-Bond (Ligand Donor)	false
OXT	OD1	ASP- 25	3.43	127.82	H-Bond (Ligand Donor)	false
N2	O	GLY- 27	3.25	164.75	H-Bond (Ligand Donor)	false
N'	O	GLY- 27	2.73	162.21	H-Bond (Ligand Donor)	false
CG2	CB	ALA- 28	4.1	0	Hydrophobic	false
C11	CB	ALA- 28	3.87	0	Hydrophobic	false
O	N	ASP- 29	3.08	166.56	H-Bond (Protein Donor)	false
O2	N	ASP- 29	3.21	177.18	H-Bond (Protein Donor)	false
C41	CB	ASP- 30	4.26	0	Hydrophobic	false
CG2	CG2	ILE- 32	4.21	0	Hydrophobic	false
CB	CG1	VAL- 47	4.22	0	Hydrophobic	false
C41	CG2	VAL- 47	3.9	0	Hydrophobic	false
N	O	GLY- 48	3.17	138.35	H-Bond (Ligand Donor)	false
N3	O	GLY- 48	2.8	157.43	H-Bond (Ligand Donor)	false
CD1	CD1	ILE- 50	4.09	0	Hydrophobic	false
CT2	CD1	ILE- 50	4.17	0	Hydrophobic	false
CT4	CD1	ILE- 50	4.25	0	Hydrophobic	false
CG2	CG1	ILE- 50	4.15	0	Hydrophobic	false
C11	CD1	ILE- 50	3.67	0	Hydrophobic	false
C5	CB	PRO- 81	4.39	0	Hydrophobic	false
CT2	CG	PRO- 81	4.31	0	Hydrophobic	false
C7	CG	PRO- 81	3.72	0	Hydrophobic	false
CE1	CG	PRO- 81	4.18	0	Hydrophobic	false
CT3	CG1	ILE- 82	3.68	0	Hydrophobic	false
CZ	CD1	ILE- 82	3.44	0	Hydrophobic	false
C5	CD1	ILE- 82	3.79	0	Hydrophobic	false
CG2	CD1	ILE- 84	3.87	0	Hydrophobic	false
CG	CG2	ILE- 84	4.41	0	Hydrophobic	false
CT4	CD1	ILE- 84	3.53	0	Hydrophobic	false
C11	CD1	ILE- 84	3.6	0	Hydrophobic	false