scPDB - 4a6c entry

Protein Data Bank Entry:

PDB ID : 4a6c

Resolution :1.500 Å

Experimental Method : X-ray

Deposition Date : 2011-11-01

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_HV1Y2
AC:	P35963
Organism:	Human immunodeficiency virus type 1 group M subtype B
Reign:	Viruses
TaxID:	362651
EC Number:	3.4.23.16

Chains:

Chain Name:	Percentage of Residues within binding site
A	48 %
B	52 %

Ligand binding site composition:

B-Factor:	10.816
Number of residues:	47
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.000	894.375

% Hydrophobic	% Polar
40.00	60.00
According to VolSite

Ligand :

HET Code:	QG9
Formula:	C43H51N5O6
Molecular weight:	733.895 g/mol
DrugBank ID:	-
Buried Surface Area:	60.9 %
Polar Surface area:	144.33 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	4
Rings:	6
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	15

Mass center Coordinates

X	Y	Z
13.4368	22.336	6.60591

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
C35	CD2	LEU- 23	4.26	0	Hydrophobic	false
O17	OD2	ASP- 25	2.6	141.73	H-Bond (Ligand Donor)	false
C4	CB	ALA- 28	4.41	0	Hydrophobic	false
C16	CB	ALA- 28	3.95	0	Hydrophobic	false
C14	CB	ASP- 29	4.27	0	Hydrophobic	false
C15	CG2	VAL- 32	3.57	0	Hydrophobic	false
C9	CB	ILE- 47	4.01	0	Hydrophobic	false
C13	CG2	ILE- 47	3.69	0	Hydrophobic	false
C24	CD1	ILE- 50	3.97	0	Hydrophobic	false
C23	CG1	ILE- 50	3.71	0	Hydrophobic	false
C46	CG1	ILE- 50	3.79	0	Hydrophobic	false
C47	CG1	ILE- 50	4.06	0	Hydrophobic	false
C14	CD1	LEU- 76	3.82	0	Hydrophobic	false
C34	CG	PRO- 81	3.59	0	Hydrophobic	false
C50	CG	PRO- 81	3.56	0	Hydrophobic	false
C31	CB	THR- 82	3.88	0	Hydrophobic	false
C31	CB	THR- 82	3.88	0	Hydrophobic	false
C19	CG1	VAL- 84	4.43	0	Hydrophobic	false
C35	CG1	VAL- 84	4.27	0	Hydrophobic	false
C27	CD2	LEU- 123	3.68	0	Hydrophobic	false
N37	O	GLY- 127	3.17	140.95	H-Bond (Ligand Donor)	false
C47	CB	ALA- 128	3.89	0	Hydrophobic	false
C43	CB	ASP- 129	4.37	0	Hydrophobic	false
O44	N	ASP- 129	2.94	162.35	H-Bond (Protein Donor)	false
C48	CB	ASP- 130	4.32	0	Hydrophobic	false
C47	CG2	VAL- 132	4.1	0	Hydrophobic	false
C48	CG2	VAL- 132	3.9	0	Hydrophobic	false
C46	CD1	ILE- 147	3.79	0	Hydrophobic	false
C48	CD1	ILE- 147	4.08	0	Hydrophobic	false
N40	O	GLY- 148	2.97	169.36	H-Bond (Ligand Donor)	false
C16	CD1	ILE- 150	4.44	0	Hydrophobic	false
C33	CG1	ILE- 150	4.15	0	Hydrophobic	false
C20	CD1	ILE- 150	3.98	0	Hydrophobic	false
C25	CG	PRO- 181	3.46	0	Hydrophobic	false
C25	CB	THR- 182	4.08	0	Hydrophobic	false
C47	CG2	VAL- 184	4.25	0	Hydrophobic	false
C26	CG1	VAL- 184	3.66	0	Hydrophobic	false
O12	O	HOH- 2023	2.84	161.68	H-Bond (Protein Donor)	false