scPDB - 4e2x entry

Protein Data Bank Entry:

PDB ID : 4e2x

Resolution :1.400 Å

Experimental Method : X-ray

Deposition Date : 2012-03-09

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Methyltransferase
ID:	B5L6K6_MICCH
AC:	B5L6K6
Organism:	Micromonospora chalcea
Reign:	Bacteria
TaxID:	1874
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	9.054
Number of residues:	37
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.818	570.375

% Hydrophobic	% Polar
45.56	54.44
According to VolSite

Ligand :

HET Code:	TYD
Formula:	C10H13N2O11P2
Molecular weight:	399.165 g/mol
DrugBank ID:	DB03103
Buried Surface Area:	74.57 %
Polar Surface area:	220.27 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	2
Rings:	2
Aromatic rings:	0
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
-23.4638	9.5326	3.48856

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
O1A	OH	TYR- 78	2.7	164.54	H-Bond (Protein Donor)	false
C5M	CB	SER- 83	4.11	0	Hydrophobic	false
C5'	CG2	THR- 326	3.83	0	Hydrophobic	false
O1B	N	ALA- 327	2.84	161.56	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 328	2.86	0	Ionic (Protein Cationic)	false
O2B	NZ	LYS- 328	2.71	0	Ionic (Protein Cationic)	false
O2B	N	LYS- 328	3.46	165.62	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 328	2.71	170.34	H-Bond (Protein Donor)	false
O3'	OD2	ASP- 348	3.31	121.84	H-Bond (Ligand Donor)	false
O3'	OD1	ASP- 348	2.66	178.44	H-Bond (Ligand Donor)	false
O2	N	THR- 349	3	135.46	H-Bond (Protein Donor)	false
O3'	OG1	THR- 350	3.26	123.49	H-Bond (Protein Donor)	false
O3'	NZ	LYS- 353	2.76	169.65	H-Bond (Protein Donor)	false
C5'	CB	ALA- 383	4.08	0	Hydrophobic	false
O2A	ND2	ASN- 385	2.9	152.92	H-Bond (Protein Donor)	false
O1A	NE2	HIS- 386	2.83	169.7	H-Bond (Protein Donor)	false
C5M	CB	HIS- 386	3.85	0	Hydrophobic	false
C5M	CG	GLU- 389	4.15	0	Hydrophobic	false
C5M	CG1	ILE- 390	4.26	0	Hydrophobic	false
O4	NZ	LYS- 393	2.83	132.83	H-Bond (Protein Donor)	false
O1B	O	HOH- 615	2.72	157.43	H-Bond (Protein Donor)	false