scPDB - 4cav entry

Protein Data Bank Entry:

PDB ID : 4cav

Resolution :1.890 Å

Experimental Method : X-ray

Deposition Date : 2013-10-09

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:	NMT_ASPFU
AC:	Q9UVX3
Organism:	Neosartorya fumigata
Reign:	Eukaryota
TaxID:	330879
EC Number:	2.3.1.97

Chains:

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

Ligand binding site composition:

B-Factor:	19.114
Number of residues:	46
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.671	438.750

% Hydrophobic	% Polar
75.38	24.62
According to VolSite

Ligand :

HET Code:	MYA
Formula:	C35H58N7O17P3S
Molecular weight:	973.858 g/mol
DrugBank ID:	DB02180
Buried Surface Area:	63.13 %
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:	32

Mass center Coordinates

X	Y	Z
-3.06451	7.99116	-14.4034

Binding mode :

What is Poseview ?

2D View
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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
C2	CZ	TYR- 147	3.94	0	Hydrophobic	false
C6	CD2	TYR- 147	3.43	0	Hydrophobic	false
C6M	CD1	ILE- 193	4.35	0	Hydrophobic	false
CCM	CG2	VAL- 210	4.41	0	Hydrophobic	false
CEM	CG2	VAL- 210	4.1	0	Hydrophobic	false
C8M	CG2	ILE- 212	3.96	0	Hydrophobic	false
CCM	CD1	ILE- 212	3.7	0	Hydrophobic	false
C5M	CG2	ILE- 212	4.04	0	Hydrophobic	false
CBM	CG1	ILE- 212	3.91	0	Hydrophobic	false
N4	O	LEU- 215	2.73	175.33	H-Bond (Ligand Donor)	false
C13	CD2	LEU- 215	3.98	0	Hydrophobic	false
C14	CG	LEU- 215	3.7	0	Hydrophobic	false
C4M	CD2	LEU- 215	3.89	0	Hydrophobic	false
C6M	CD2	LEU- 215	4.28	0	Hydrophobic	false
O2M	N	LEU- 215	3.28	154.42	H-Bond (Protein Donor)	false
O9	N	ILE- 217	3	160.23	H-Bond (Protein Donor)	false
C14	CD1	ILE- 217	3.67	0	Hydrophobic	false
C10	CD	ARG- 222	3.97	0	Hydrophobic	false
O4A	N	SER- 223	2.81	153.25	H-Bond (Protein Donor)	false
O1A	N	ARG- 225	2.72	147.62	H-Bond (Protein Donor)	false
O7A	NH1	ARG- 225	2.62	153.06	H-Bond (Protein Donor)	false
O7A	NH2	ARG- 225	3.47	121.59	H-Bond (Protein Donor)	false
O8A	NH1	ARG- 225	3.46	127.25	H-Bond (Protein Donor)	false
O8A	NH2	ARG- 225	2.79	152.75	H-Bond (Protein Donor)	false
O7A	CZ	ARG- 225	3.44	0	Ionic (Protein Cationic)	false
O8A	CZ	ARG- 225	3.54	0	Ionic (Protein Cationic)	false
C12	CB	THR- 227	4.43	0	Hydrophobic	false
C1X	CG2	THR- 227	3.84	0	Hydrophobic	false
C4X	CB	THR- 227	4.24	0	Hydrophobic	false
O2A	OG1	THR- 227	2.92	147.42	H-Bond (Protein Donor)	false
O2A	N	THR- 227	2.78	160.9	H-Bond (Protein Donor)	false
CBM	CG2	ILE- 231	4.17	0	Hydrophobic	false
C7M	CG1	ILE- 231	3.62	0	Hydrophobic	false
C9M	CG2	ILE- 231	3.8	0	Hydrophobic	false
CBM	CG2	ILE- 234	4.22	0	Hydrophobic	false
CCM	CB	THR- 235	4.43	0	Hydrophobic	false
CDM	CG2	THR- 235	4.24	0	Hydrophobic	false
CEM	CB	CYS- 238	3.55	0	Hydrophobic	false
CFM	CE1	TYR- 239	3.76	0	Hydrophobic	false
CFM	CG2	ILE- 243	4.45	0	Hydrophobic	false
CCM	CB	ALA- 246	3.81	0	Hydrophobic	false
CDM	CB	ALA- 246	3.68	0	Hydrophobic	false
C7M	CZ	TYR- 248	3.95	0	Hydrophobic	false
C9M	CE1	TYR- 248	3.63	0	Hydrophobic	false
C5M	CD2	TYR- 248	3.44	0	Hydrophobic	false
S1	CB	ALA- 250	4.24	0	Hydrophobic	false
C9M	CD1	TYR- 462	4.3	0	Hydrophobic	false
CAM	CB	TYR- 462	3.88	0	Hydrophobic	false
CFM	CD2	TYR- 462	3.47	0	Hydrophobic	false
O4A	O	HOH- 2176	3.15	137.88	H-Bond (Protein Donor)	false