scPDB - 3gga entry

Protein Data Bank Entry:

PDB ID : 3gga

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2009-02-27

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_HV1B1
AC:	P03366
Organism:	Human immunodeficiency virus type 1 group M subtype B
Reign:	Viruses
TaxID:	11678
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
G	50 %
H	50 %

Ligand binding site composition:

B-Factor:	24.491
Number of residues:	42
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.126	958.500

% Hydrophobic	% Polar
44.37	55.63
According to VolSite

Ligand :

HET Code:	GGW
Formula:	C39H53N5O7
Molecular weight:	703.867 g/mol
DrugBank ID:	-
Buried Surface Area:	62.86 %
Polar Surface area:	167.97 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	5
Rings:	3
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	18

Mass center Coordinates

X	Y	Z
28.6072	4.74804	-0.744588

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
C21	CD2	LEU- 23	4.01	0	Hydrophobic	false
C35	CD2	LEU- 23	4.37	0	Hydrophobic	false
C37	CD2	LEU- 23	4.38	0	Hydrophobic	false
O13	OD1	ASP- 25	3	123.15	H-Bond (Ligand Donor)	false
O13	OD2	ASP- 25	2.68	167	H-Bond (Ligand Donor)	false
N9	O	GLY- 27	3.07	151.69	H-Bond (Ligand Donor)	false
N22	O	GLY- 27	3.05	142.34	H-Bond (Ligand Donor)	false
C33	CB	ALA- 28	3.79	0	Hydrophobic	false
C50	CB	ALA- 28	3.74	0	Hydrophobic	false
C1	CB	ASP- 29	4.17	0	Hydrophobic	false
O4	N	ASP- 29	2.95	176.84	H-Bond (Protein Donor)	false
O28	N	ASP- 29	3.14	169.94	H-Bond (Protein Donor)	false
C51	CB	ASP- 30	4.45	0	Hydrophobic	false
C33	CG2	VAL- 32	4.45	0	Hydrophobic	false
C50	CG1	VAL- 32	4.37	0	Hydrophobic	false
C34	CD1	ILE- 47	3.98	0	Hydrophobic	false
C49	CD1	ILE- 47	3.91	0	Hydrophobic	false
C51	CD1	ILE- 47	4.46	0	Hydrophobic	false
N5	O	GLY- 48	2.99	168.63	H-Bond (Ligand Donor)	false
N26	O	GLY- 48	2.76	156.47	H-Bond (Ligand Donor)	false
C17	CD1	ILE- 50	4.26	0	Hydrophobic	false
C32	CG1	ILE- 50	4.03	0	Hydrophobic	false
C34	CG1	ILE- 50	3.68	0	Hydrophobic	false
C41	CG1	ILE- 50	4.43	0	Hydrophobic	false
C49	CG1	ILE- 50	3.96	0	Hydrophobic	false
C50	CD1	ILE- 50	4.42	0	Hydrophobic	false
C45	CB	PRO- 81	4.13	0	Hydrophobic	false
C18	CG	PRO- 81	3.7	0	Hydrophobic	false
C40	CG	PRO- 81	3.75	0	Hydrophobic	false
C43	CG	PRO- 81	3.63	0	Hydrophobic	false
C19	CG1	VAL- 82	3.66	0	Hydrophobic	false
C36	CG2	VAL- 82	3.93	0	Hydrophobic	false
C32	CD1	ILE- 84	3.84	0	Hydrophobic	false
C35	CD1	ILE- 84	4.06	0	Hydrophobic	false
C41	CD1	ILE- 84	4.49	0	Hydrophobic	false
C50	CD1	ILE- 84	4.03	0	Hydrophobic	false
C17	CD1	ILE- 84	4.04	0	Hydrophobic	false