scPDB - 3ndj entry

Protein Data Bank Entry:

PDB ID : 3ndj

Resolution :1.500 Å

Experimental Method : X-ray

Deposition Date : 2010-06-07

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:	5.673
Number of residues:	52
Including
Standard Amino Acids:	47
Non Standard Amino Acids:	1
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.658	469.125

% Hydrophobic	% Polar
44.60	55.40
According to VolSite

Ligand :

HET Code:	JHZ
Formula:	C17H26N3O13P2
Molecular weight:	542.348 g/mol
DrugBank ID:	-
Buried Surface Area:	79.69 %
Polar Surface area:	260.37 Å2

Number of
H-Bond Acceptors:	13
H-Bond Donors:	3
Rings:	3
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
22.6444	11.6581	-1.82846

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
C1	CD1	TYR- 78	3.51	0	Hydrophobic	false
C2	CG	TYR- 78	4.15	0	Hydrophobic	false
C5	CZ	TYR- 78	4.1	0	Hydrophobic	false
C6	CE2	TYR- 78	3.87	0	Hydrophobic	false
C3M	CD2	TYR- 78	4.24	0	Hydrophobic	false
O1P	OH	TYR- 78	2.67	147.65	H-Bond (Protein Donor)	false
C5A	CB	SER- 83	4.01	0	Hydrophobic	false
C6	CB	ASN- 177	3.67	0	Hydrophobic	false
N3	NE2	HIS- 181	2.75	154.76	H-Bond (Ligand Donor)	false
N3	OH	TYR- 222	2.92	159.14	H-Bond (Ligand Donor)	false
N3	OE1	GLU- 224	2.69	163.45	H-Bond (Ligand Donor)	false
N3	OE1	GLU- 224	2.69	0	Ionic (Ligand Cationic)	false
O4	NE2	HIS- 225	2.82	162.47	H-Bond (Protein Donor)	false
C5X	CG2	THR- 326	3.75	0	Hydrophobic	false
O3P	N	ALA- 327	2.78	165.06	H-Bond (Protein Donor)	false
C2	CB	ALA- 327	4.16	0	Hydrophobic	false
O2P	NZ	LYS- 328	2.96	0	Ionic (Protein Cationic)	false
O4P	NZ	LYS- 328	2.92	0	Ionic (Protein Cationic)	false
O4P	NZ	LYS- 328	2.92	166.13	H-Bond (Protein Donor)	false
O3X	OD1	ASP- 348	2.67	161.3	H-Bond (Ligand Donor)	false
O21	N	THR- 349	3.09	131.55	H-Bond (Protein Donor)	false
O3X	OG1	THR- 350	3.39	124.31	H-Bond (Protein Donor)	false
O3X	NZ	LYS- 353	2.68	164.87	H-Bond (Protein Donor)	false
C5X	CB	ALA- 383	4.23	0	Hydrophobic	false
O2P	ND2	ASN- 385	2.86	157.66	H-Bond (Protein Donor)	false
O1P	NE2	HIS- 386	2.8	167.21	H-Bond (Protein Donor)	false
C5A	CB	HIS- 386	3.89	0	Hydrophobic	false
C5A	CG	GLU- 389	4.38	0	Hydrophobic	false
C5A	CG1	ILE- 390	4.4	0	Hydrophobic	false
O41	NZ	LYS- 393	2.77	132.48	H-Bond (Protein Donor)	false
O3P	O	HOH- 461	2.79	152.64	H-Bond (Protein Donor)	false