scPDB - 1sd2 entry

Protein Data Bank Entry:

PDB ID : 1sd2

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2004-02-12

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	S-methyl-5'-thioadenosine phosphorylase
ID:	MTAP_HUMAN
AC:	Q13126
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:	24.866
Number of residues:	34
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.365	432.000

% Hydrophobic	% Polar
55.47	44.53
According to VolSite

Ligand :

HET Code:	MTH
Formula:	C12H16N4O3S
Molecular weight:	296.345 g/mol
DrugBank ID:	DB02933
Buried Surface Area:	72.99 %
Polar Surface area:	131.72 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	3

Mass center Coordinates

X	Y	Z
60.0213	16.1587	29.0243

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
CS	CG2	THR- 18	4.26	0	Hydrophobic	false
C3'	CG	PRO- 69	3.98	0	Hydrophobic	false
C1'	CB	ALA- 94	4.15	0	Hydrophobic	false
S5'	CZ	PHE- 177	3.92	0	Hydrophobic	false
C2'	CB	ASN- 195	4.36	0	Hydrophobic	false
C2'	CG	MET- 196	3.72	0	Hydrophobic	false
C3'	SD	MET- 196	3.76	0	Hydrophobic	false
O2'	N	MET- 196	2.91	147.44	H-Bond (Protein Donor)	false
N6	OD1	ASP- 220	3.35	150.85	H-Bond (Ligand Donor)	false
N6	OD1	ASP- 222	2.98	167.45	H-Bond (Ligand Donor)	false
CS	CG1	VAL- 233	4.37	0	Hydrophobic	false
S5'	CG1	VAL- 236	3.94	0	Hydrophobic	false
CS	CD2	LEU- 237	4.4	0	Hydrophobic	false
N1	O	HOH- 286	2.83	179.96	H-Bond (Protein Donor)	false