scPDB - 4c2y entry

Protein Data Bank Entry:

PDB ID : 4c2y

Resolution :1.640 Å

Experimental Method : X-ray

Deposition Date : 2013-08-20

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 1
ID:	NMT1_HUMAN
AC:	P30419
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	17.948
Number of residues:	59
Including
Standard Amino Acids:	53
Non Standard Amino Acids:	1
Water Molecules:	5
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
1.208	945.000

% Hydrophobic	% Polar
55.36	44.64
According to VolSite

Ligand :

HET Code:	MYA
Formula:	C35H58N7O17P3S
Molecular weight:	973.858 g/mol
DrugBank ID:	DB02180
Buried Surface Area:	71.9 %
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
-19.7278	8.40181	-5.65094

Binding mode :

What is Poseview ?

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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
O7A	N	PHE- 119	2.96	131.85	H-Bond (Protein Donor)	false
O8A	N	PHE- 119	3.35	160.87	H-Bond (Protein Donor)	false
N3A	NE1	TRP- 120	3.1	163.8	H-Bond (Protein Donor)	false
O7A	N	TRP- 120	2.8	166.31	H-Bond (Protein Donor)	false
C7M	CZ2	TRP- 120	3.7	0	Hydrophobic	false
C9M	CH2	TRP- 120	3.7	0	Hydrophobic	false
C2	CE1	TYR- 180	4.02	0	Hydrophobic	false
C6	CD1	TYR- 180	3.54	0	Hydrophobic	false
C2	CG2	VAL- 181	3.94	0	Hydrophobic	false
C6	CG2	VAL- 181	3.91	0	Hydrophobic	false
CEM	CG2	VAL- 243	4.23	0	Hydrophobic	false
C8M	CG2	ILE- 245	3.86	0	Hydrophobic	false
CCM	CG1	ILE- 245	3.78	0	Hydrophobic	false
C5M	CG2	ILE- 245	3.84	0	Hydrophobic	false
CAM	CG1	ILE- 245	3.73	0	Hydrophobic	false
N4	O	LEU- 248	2.8	154.4	H-Bond (Ligand Donor)	false
C13	CD2	LEU- 248	4.24	0	Hydrophobic	false
C14	CG	LEU- 248	3.6	0	Hydrophobic	false
C4M	CB	LEU- 248	3.88	0	Hydrophobic	false
C6M	CD2	LEU- 248	4.2	0	Hydrophobic	false
O2M	N	LEU- 248	3.19	149.52	H-Bond (Protein Donor)	false
O9	N	VAL- 250	2.96	168.96	H-Bond (Protein Donor)	false
C14	CG2	VAL- 250	3.78	0	Hydrophobic	false
C10	CD	ARG- 255	3.53	0	Hydrophobic	false
O4A	N	SER- 256	2.78	160.38	H-Bond (Protein Donor)	false
O1A	N	ARG- 258	3.1	141.61	H-Bond (Protein Donor)	false
O8A	NH2	ARG- 258	2.94	175.37	H-Bond (Protein Donor)	false
O8A	CZ	ARG- 258	3.76	0	Ionic (Protein Cationic)	false
O2A	N	ALA- 260	2.74	160.52	H-Bond (Protein Donor)	false
C12	CB	ALA- 260	3.66	0	Hydrophobic	false
C4X	CG	PRO- 261	4.07	0	Hydrophobic	false
C6M	CG1	ILE- 264	4.06	0	Hydrophobic	false
CBM	CG2	ILE- 264	4.29	0	Hydrophobic	false
C9M	CG2	ILE- 264	3.92	0	Hydrophobic	false
CBM	CG2	ILE- 267	4.17	0	Hydrophobic	false
CCM	CB	THR- 268	4.38	0	Hydrophobic	false
CDM	CG2	THR- 268	4.19	0	Hydrophobic	false
CEM	CG1	VAL- 271	3.64	0	Hydrophobic	false
CAM	CB	ALA- 279	3.95	0	Hydrophobic	false
CDM	CB	ALA- 279	3.73	0	Hydrophobic	false
C3M	CB	TYR- 281	4.19	0	Hydrophobic	false
C7M	CE2	TYR- 281	3.98	0	Hydrophobic	false
C8M	CD1	TYR- 281	3.97	0	Hydrophobic	false
C5M	CD2	TYR- 281	3.6	0	Hydrophobic	false
C9M	CE1	TYR- 281	3.71	0	Hydrophobic	false
S1	CB	ALA- 283	4.21	0	Hydrophobic	false
CAM	CD2	TYR- 479	3.79	0	Hydrophobic	false
CDM	CD1	TYR- 479	3.58	0	Hydrophobic	false