scPDB - 3ggx entry

Protein Data Bank Entry:

PDB ID : 3ggx

Resolution :2.700 Å

Experimental Method : X-ray

Deposition Date : 2009-03-02

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
F	2 %
G	45 %
H	52 %

Ligand binding site composition:

B-Factor:	22.098
Number of residues:	44
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.110	1042.875

% Hydrophobic	% Polar
39.16	60.84
According to VolSite

Ligand :

HET Code:	GGX
Formula:	C47H59N7O6
Molecular weight:	818.015 g/mol
DrugBank ID:	-
Buried Surface Area:	54.66 %
Polar Surface area:	166.08 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	4
Rings:	5
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	19

Mass center Coordinates

X	Y	Z
6.27658	54.7589	29.6157

Binding mode :

What is Poseview ?

2D View
3D View

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
DuAr	CZ	ARG- 8	3.1	157.5	Pi/Cation	false
C50	CD	ARG- 8	3.52	0	Hydrophobic	false
C14	CD2	LEU- 23	4.08	0	Hydrophobic	false
C42	CD2	LEU- 23	3.68	0	Hydrophobic	false
O54	OD1	ASP- 25	3.33	126.82	H-Bond (Ligand Donor)	false
N4	O	GLY- 27	3.07	165.18	H-Bond (Ligand Donor)	false
N28	O	GLY- 27	2.53	147.65	H-Bond (Ligand Donor)	false
C2	CB	ALA- 28	4.48	0	Hydrophobic	false
C12	CB	ALA- 28	3.87	0	Hydrophobic	false
C38	CB	ALA- 28	4.31	0	Hydrophobic	false
C39	CB	ALA- 28	4.41	0	Hydrophobic	false
O27	N	ASP- 29	2.8	154.62	H-Bond (Protein Donor)	false
O41	N	ASP- 29	2.96	160.78	H-Bond (Protein Donor)	false
C36	CB	ASP- 29	4.05	0	Hydrophobic	false
C38	CD1	ILE- 47	4.4	0	Hydrophobic	false
N33	O	GLY- 48	2.95	170.68	H-Bond (Ligand Donor)	false
C39	CD1	ILE- 50	4.04	0	Hydrophobic	false
C40	CG2	ILE- 50	3.99	0	Hydrophobic	false
C53	CB	ILE- 50	3.73	0	Hydrophobic	false
C17	CG1	ILE- 50	4.15	0	Hydrophobic	false
C52	CB	PRO- 81	3.88	0	Hydrophobic	false
C60	CB	PRO- 81	4.44	0	Hydrophobic	false
C16	CG	PRO- 81	3.9	0	Hydrophobic	false
C45	CG	PRO- 81	3.25	0	Hydrophobic	false
C52	CG1	VAL- 82	4.34	0	Hydrophobic	false
C15	CG2	VAL- 82	4.24	0	Hydrophobic	false
C49	CG1	VAL- 82	3.64	0	Hydrophobic	false
C43	CG1	VAL- 82	3.71	0	Hydrophobic	false
C39	CD1	ILE- 84	4.21	0	Hydrophobic	false
C53	CD1	ILE- 84	4.48	0	Hydrophobic	false
C19	CD1	ILE- 84	3.98	0	Hydrophobic	false
C18	CD1	ILE- 84	3.78	0	Hydrophobic	false
C26	CD1	ILE- 84	3.87	0	Hydrophobic	false