scPDB - 3fx5 entry

Protein Data Bank Entry:

PDB ID : 3fx5

Resolution :0.930 Å

Experimental Method : X-ray

Deposition Date : 2009-01-20

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	48 %
B	52 %

Ligand binding site composition:

B-Factor:	9.024
Number of residues:	45
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.671	705.375

% Hydrophobic	% Polar
38.28	61.72
According to VolSite

Ligand :

HET Code:	KNI
Formula:	C33H41N5O6S2
Molecular weight:	667.839 g/mol
DrugBank ID:	-
Buried Surface Area:	67.61 %
Polar Surface area:	200.56 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	4
Rings:	4
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	14

Mass center Coordinates

X	Y	Z
14.2048	21.1839	15.8328

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
C33	CD2	LEU- 23	3.86	0	Hydrophobic	false
O4	OD2	ASP- 25	2.64	150.23	H-Bond (Protein Donor)	false
C23	CB	ALA- 28	4.17	0	Hydrophobic	false
C25	CB	ALA- 28	4.19	0	Hydrophobic	false
C25	CB	ASP- 30	4.28	0	Hydrophobic	false
C23	CG2	VAL- 32	4.08	0	Hydrophobic	false
C25	CG2	VAL- 32	4.38	0	Hydrophobic	false
C24	CD1	ILE- 47	4.02	0	Hydrophobic	false
S2	CG1	ILE- 50	4.07	0	Hydrophobic	false
S1	CG1	ILE- 50	3.74	0	Hydrophobic	false
C2	CG	PRO- 81	4.4	0	Hydrophobic	false
C4	CB	PRO- 81	4.26	0	Hydrophobic	false
C31	CG	PRO- 81	4.08	0	Hydrophobic	false
C31	CG2	VAL- 82	3.75	0	Hydrophobic	false
C8	CG2	VAL- 82	3.75	0	Hydrophobic	false
C23	CD1	ILE- 84	3.72	0	Hydrophobic	false
C29	CD1	ILE- 84	3.59	0	Hydrophobic	false
O2	OD1	ASP- 125	2.6	155.54	H-Bond (Ligand Donor)	false
O2	OD2	ASP- 125	3.16	133.66	H-Bond (Ligand Donor)	false
N3	O	GLY- 127	3.08	154.64	H-Bond (Ligand Donor)	false
C15	CB	ALA- 128	4.5	0	Hydrophobic	false
C27	CB	ALA- 128	3.95	0	Hydrophobic	false
O3	N	ASP- 129	2.9	154	H-Bond (Protein Donor)	false
C27	CB	ASP- 130	3.94	0	Hydrophobic	false
C27	CG2	VAL- 132	3.61	0	Hydrophobic	false
C12	CB	ILE- 147	4.38	0	Hydrophobic	false
S1	CD1	ILE- 147	3.94	0	Hydrophobic	false
N2	O	GLY- 148	2.83	137.23	H-Bond (Ligand Donor)	false
C23	CD1	ILE- 150	4.08	0	Hydrophobic	false
C24	CG2	ILE- 150	3.69	0	Hydrophobic	false
S2	CG	PRO- 181	3.88	0	Hydrophobic	false
S1	CD1	ILE- 184	4.26	0	Hydrophobic	false
S2	CD1	ILE- 184	4.11	0	Hydrophobic	false
N5	O	HOH- 608	3.08	169.2	H-Bond (Ligand Donor)	false