scPDB - 4b12 entry

Protein Data Bank Entry:

PDB ID : 4b12

Resolution :1.790 Å

Experimental Method : X-ray

Deposition Date : 2012-07-06

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
B	100 %

Ligand binding site composition:

B-Factor:	16.736
Number of residues:	37
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.336	2190.375

% Hydrophobic	% Polar
52.23	47.77
According to VolSite

Ligand :

HET Code:	C23
Formula:	C23H26NO3
Molecular weight:	364.457 g/mol
DrugBank ID:	-
Buried Surface Area:	65.11 %
Polar Surface area:	56.05 Å2

Number of
H-Bond Acceptors:	2
H-Bond Donors:	1
Rings:	4
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
15.3735	24.6636	32.9938

Binding mode :

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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
C22	CG1	VAL- 96	3.78	0	Hydrophobic	false
C18	CB	ASP- 98	3.55	0	Hydrophobic	false
C19	CB	PHE- 103	3.89	0	Hydrophobic	false
C	CZ	PHE- 105	3.65	0	Hydrophobic	false
C13	CB	TYR- 211	4.19	0	Hydrophobic	false
C	CE2	TYR- 211	4.11	0	Hydrophobic	false
C15	CZ	TYR- 211	3.49	0	Hydrophobic	false
C4	CB	TYR- 211	3.22	0	Hydrophobic	false
C9	CZ	TYR- 315	4.45	0	Hydrophobic	false
C9	CD2	LEU- 317	4.04	0	Hydrophobic	false
C9	CE2	TYR- 334	4.12	0	Hydrophobic	false
C5	CE2	TYR- 334	3.48	0	Hydrophobic	false
C4	CB	ASN- 365	3.88	0	Hydrophobic	false
C7	CD2	LEU- 367	4.29	0	Hydrophobic	false
C6	CG	LEU- 367	3.71	0	Hydrophobic	false
C12	CD2	LEU- 388	3.57	0	Hydrophobic	false
N	O	LEU- 410	3.08	143.72	H-Bond (Ligand Donor)	false
N	O	LEU- 410	3.08	0	Ionic (Ligand Cationic)	false
N	OXT	LEU- 410	3.51	0	Ionic (Ligand Cationic)	false
N	O	HOH- 2112	3.32	124.84	H-Bond (Ligand Donor)	false