scPDB - 3ckt entry

Protein Data Bank Entry:

PDB ID : 3ckt

Resolution :1.650 Å

Experimental Method : X-ray

Deposition Date : 2008-03-17

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	53 %
B	47 %

Ligand binding site composition:

B-Factor:	18.419
Number of residues:	46
Including
Standard Amino Acids:	45
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.181	951.750

% Hydrophobic	% Polar
45.04	54.96
According to VolSite

Ligand :

HET Code:	YDP
Formula:	C28H38N5O6S2
Molecular weight:	604.761 g/mol
DrugBank ID:	-
Buried Surface Area:	65.1 %
Polar Surface area:	194.3 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	12

Mass center Coordinates

X	Y	Z
5.89037	2.27812	-14.0873

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
C11	CD2	LEU- 23	3.56	0	Hydrophobic	false
C12	CD2	LEU- 23	3.68	0	Hydrophobic	false
N22	OD1	ASP- 25	2.83	135.65	H-Bond (Ligand Donor)	false
N22	OD2	ASP- 25	2.94	144.22	H-Bond (Ligand Donor)	false
N22	OD2	ASP- 25	2.75	145.93	H-Bond (Ligand Donor)	false
N22	OD1	ASP- 25	2.83	0	Ionic (Ligand Cationic)	false
N22	OD2	ASP- 25	2.94	0	Ionic (Ligand Cationic)	false
N22	OD1	ASP- 25	2.84	0	Ionic (Ligand Cationic)	false
N22	OD2	ASP- 25	2.75	0	Ionic (Ligand Cationic)	false
C18	CB	ALA- 28	3.5	0	Hydrophobic	false
C7	CB	ALA- 28	3.53	0	Hydrophobic	false
O2	N	ASP- 30	2.57	134.33	H-Bond (Protein Donor)	false
O3	N	ASP- 30	2.68	152.58	H-Bond (Protein Donor)	false
N2	OD1	ASP- 30	2.82	160.99	H-Bond (Ligand Donor)	false
C18	CG2	VAL- 32	3.87	0	Hydrophobic	false
C5	CB	ILE- 47	3.89	0	Hydrophobic	false
C18	CD1	ILE- 47	4.13	0	Hydrophobic	false
C3	CD1	ILE- 50	4.44	0	Hydrophobic	false
C19	CG1	ILE- 50	4.06	0	Hydrophobic	false
C28	CG2	ILE- 50	4.13	0	Hydrophobic	false
O12	N	ILE- 50	2.61	165.97	H-Bond (Protein Donor)	false
C13	CG	PRO- 81	4.04	0	Hydrophobic	false
C10	CG1	VAL- 82	4.42	0	Hydrophobic	false
C12	CG1	VAL- 82	4.11	0	Hydrophobic	false
C10	CD1	ILE- 84	4.44	0	Hydrophobic	false
C33	CD1	ILE- 84	3.65	0	Hydrophobic	false
C11	CG1	ILE- 84	4.45	0	Hydrophobic	false
C12	CD1	ILE- 84	4.04	0	Hydrophobic	false
C21	CD1	ILE- 84	4.18	0	Hydrophobic	false
C37	CD1	ILE- 84	3.63	0	Hydrophobic	false