scPDB - 4j54 entry

Protein Data Bank Entry:

PDB ID : 4j54

Resolution :1.550 Å

Experimental Method : X-ray

Deposition Date : 2013-02-07

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_HV1BR
AC:	P03367
Organism:	Human immunodeficiency virus type 1 group M subtype B
Reign:	Viruses
TaxID:	11686
EC Number:	3.4.23.16

Chains:

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

Ligand binding site composition:

B-Factor:	12.576
Number of residues:	45
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	IOD

Cavity properties

Ligandability	Volume (Å3)
0.992	756.000

% Hydrophobic	% Polar
43.75	56.25
According to VolSite

Ligand :

HET Code:	G52
Formula:	C30H40N2O9S
Molecular weight:	604.712 g/mol
DrugBank ID:	-
Buried Surface Area:	66.97 %
Polar Surface area:	141.24 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	2
Rings:	5
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
2.52095	8.05207	37.6832

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
C15	CD2	LEU- 23	4.19	0	Hydrophobic	false
C33	CD1	LEU- 23	4.35	0	Hydrophobic	false
O18	OD1	ASP- 25	2.61	164.99	H-Bond (Protein Donor)	false
O18	OD2	ASP- 25	2.52	166.1	H-Bond (Ligand Donor)	false
N20	O	GLY- 27	3.03	170.58	H-Bond (Ligand Donor)	false
C16	CB	ALA- 28	4.36	0	Hydrophobic	false
C25	CB	ALA- 28	3.97	0	Hydrophobic	false
C3	CB	ALA- 28	3.56	0	Hydrophobic	false
C27	CB	ASP- 29	4.15	0	Hydrophobic	false
C40	CB	ASP- 29	3.57	0	Hydrophobic	false
O28	N	ASP- 29	2.77	171.62	H-Bond (Protein Donor)	false
O26	N	ASN- 30	3.31	154.57	H-Bond (Protein Donor)	false
O26	ND2	ASN- 30	3.3	139.43	H-Bond (Protein Donor)	false
O39	N	ASN- 30	3.1	140.46	H-Bond (Protein Donor)	false
C40	CB	ASN- 30	4.01	0	Hydrophobic	false
C25	CD1	ILE- 32	3.78	0	Hydrophobic	false
C3	CD1	ILE- 32	3.62	0	Hydrophobic	false
C40	CG1	VAL- 47	4	0	Hydrophobic	false
C7	CB	VAL- 47	3.99	0	Hydrophobic	false
C5	CD1	ILE- 50	4.36	0	Hydrophobic	false
C14	CG1	ILE- 50	3.98	0	Hydrophobic	false
C24	CD1	ILE- 50	3.73	0	Hydrophobic	false
C37	CB	ILE- 50	4.45	0	Hydrophobic	false
C36	CG	PRO- 81	3.79	0	Hydrophobic	false
C15	CG1	VAL- 82	3.55	0	Hydrophobic	false
C34	CG1	VAL- 82	3.47	0	Hydrophobic	false
C4	CG2	VAL- 84	4.37	0	Hydrophobic	false
C15	CG1	VAL- 84	4.44	0	Hydrophobic	false
C32	CG1	VAL- 84	4.35	0	Hydrophobic	false