scPDB - 2ync entry

Protein Data Bank Entry:

PDB ID : 2ync

Resolution :1.750 Å

Experimental Method : X-ray

Deposition Date : 2012-10-13

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Glycylpeptide N-tetradecanoyltransferase
ID:	A5K1A2_PLAVS
AC:	A5K1A2
Organism:	Plasmodium vivax
Reign:	Eukaryota
TaxID:	126793
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	10.108
Number of residues:	54
Including
Standard Amino Acids:	52
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
1.351	1279.125

% Hydrophobic	% Polar
50.92	49.08
According to VolSite

Ligand :

HET Code:	YNC
Formula:	C35H54N7O17P3S
Molecular weight:	969.826 g/mol
DrugBank ID:	-
Buried Surface Area:	71.75 %
Polar Surface area:	429.68 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	31

Mass center Coordinates

X	Y	Z
40.0991	41.4293	65.878

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
O3	N	PHE- 30	2.93	129.11	H-Bond (Protein Donor)	false
N2	NE1	TRP- 31	3.14	158.57	H-Bond (Protein Donor)	false
O3	N	TRP- 31	2.87	168.67	H-Bond (Protein Donor)	false
C26	CZ2	TRP- 31	3.97	0	Hydrophobic	false
C28	CH2	TRP- 31	3.77	0	Hydrophobic	false
C17	CD1	TYR- 95	3.7	0	Hydrophobic	false
C20	CE1	TYR- 95	4.06	0	Hydrophobic	false
C17	CG2	VAL- 96	3.91	0	Hydrophobic	false
C20	CG2	VAL- 96	3.77	0	Hydrophobic	false
C27	CG1	VAL- 160	3.75	0	Hydrophobic	false
C24	CG1	VAL- 160	3.99	0	Hydrophobic	false
C30	CG2	VAL- 160	3.89	0	Hydrophobic	false
N6	O	LEU- 163	2.74	154	H-Bond (Ligand Donor)	false
O10	N	LEU- 163	3.18	144.57	H-Bond (Protein Donor)	false
C12	CD2	LEU- 163	4.11	0	Hydrophobic	false
C13	CG	LEU- 163	3.57	0	Hydrophobic	false
C23	CB	LEU- 163	3.79	0	Hydrophobic	false
C25	CD2	LEU- 163	3.93	0	Hydrophobic	false
O12	N	VAL- 165	2.96	175.29	H-Bond (Protein Donor)	false
C13	CG2	VAL- 165	3.55	0	Hydrophobic	false
C14	CB	VAL- 165	4.38	0	Hydrophobic	false
C14	CD	ARG- 170	3.58	0	Hydrophobic	false
O8	N	SER- 171	2.73	155.12	H-Bond (Protein Donor)	false
O4	NH2	ARG- 173	2.84	152.72	H-Bond (Protein Donor)	false
O4	NH1	ARG- 173	3.04	141.6	H-Bond (Protein Donor)	false
O6	N	ARG- 173	2.89	144.01	H-Bond (Protein Donor)	false
O4	CZ	ARG- 173	3.41	0	Ionic (Protein Cationic)	false
C10	CB	ALA- 175	3.68	0	Hydrophobic	false
C13	CB	ALA- 175	4.01	0	Hydrophobic	false
O15	N	ALA- 175	2.77	166.7	H-Bond (Protein Donor)	false
C8	CG	PRO- 176	3.95	0	Hydrophobic	false
C25	CG1	ILE- 179	4.12	0	Hydrophobic	false
C26	CD1	ILE- 179	4.06	0	Hydrophobic	false
C28	CG2	ILE- 179	4.13	0	Hydrophobic	false
C30	CG2	ILE- 179	4.29	0	Hydrophobic	false
C30	CG2	ILE- 182	4.22	0	Hydrophobic	false
C31	CB	THR- 183	4.21	0	Hydrophobic	false
C32	CG2	THR- 183	3.97	0	Hydrophobic	false
C31	CD1	ILE- 186	3.76	0	Hydrophobic	false
C33	CD1	ILE- 186	4.22	0	Hydrophobic	false
C34	CG2	ILE- 186	3.58	0	Hydrophobic	false
C31	CB	ALA- 194	3.8	0	Hydrophobic	false
C33	CB	ALA- 194	3.78	0	Hydrophobic	false
C22	CB	TYR- 196	4.3	0	Hydrophobic	false
C27	CD1	TYR- 196	3.93	0	Hydrophobic	false
C24	CD2	TYR- 196	3.78	0	Hydrophobic	false
C28	CE1	TYR- 196	3.73	0	Hydrophobic	false
S	CB	ALA- 198	4.01	0	Hydrophobic	false
C29	CD1	TYR- 393	3.86	0	Hydrophobic	false
C32	CD2	TYR- 393	3.34	0	Hydrophobic	false