scPDB - 4ndn entry

Protein Data Bank Entry:

PDB ID : 4ndn

Resolution :2.340 Å

Experimental Method : X-ray

Deposition Date : 2013-10-27

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	S-adenosylmethionine synthase isoform type-2
ID:	METK2_HUMAN
AC:	P31153
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.5.1.6

Chains:

Chain Name:	Percentage of Residues within binding site
C	53 %
D	47 %

Ligand binding site composition:

B-Factor:	44.736
Number of residues:	48
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	2
Water Molecules:	3
Cofactors:
Metals:	MG MG

Cavity properties

Ligandability	Volume (Å3)
0.667	442.125

% Hydrophobic	% Polar
54.20	45.80
According to VolSite

Ligand :

HET Code:	SAM
Formula:	C15H23N6O5S
Molecular weight:	399.445 g/mol
DrugBank ID:	DB00118
Buried Surface Area:	74.58 %
Polar Surface area:	189.77 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	2
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
24.5914	-24.105	-58.9294

Binding mode :

What is Poseview ?

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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
CA	CB	ALA- 55	3.86	0	Hydrophobic	false
OXT	NE2	GLN- 113	2.74	167.36	H-Bond (Protein Donor)	false
CB	CD1	ILE- 117	3.88	0	Hydrophobic	false
CE	CD1	ILE- 117	3.53	0	Hydrophobic	false
O2'	OD2	ASP- 179	3.23	136.65	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 179	2.58	160.35	H-Bond (Ligand Donor)	false
C4'	CD	LYS- 181	3.79	0	Hydrophobic	false
C1'	CD	LYS- 181	4.03	0	Hydrophobic	false
N1	OG	SER- 247	2.71	149.26	H-Bond (Protein Donor)	false
N6	O	ARG- 249	2.9	133.06	H-Bond (Ligand Donor)	false
DuAr	DuAr	PHE- 250	3.63	0	Aromatic Face/Face	false
C1'	CZ	PHE- 250	3.54	0	Hydrophobic	false
C3'	CB	ASP- 258	3.79	0	Hydrophobic	false
CB	CB	ASP- 258	4.08	0	Hydrophobic	false
SD	CB	ASP- 258	4	0	Hydrophobic	false
O3'	OD2	ASP- 258	3.04	157.59	H-Bond (Ligand Donor)	false
OXT	NZ	LYS- 289	3.86	0	Ionic (Protein Cationic)	false
CE	CD1	ILE- 322	4.19	0	Hydrophobic	false
O	O	HOH- 504	2.93	179.97	H-Bond (Protein Donor)	false
O	O	HOH- 528	3.01	145.58	H-Bond (Protein Donor)	false