scPDB - 1xwf entry

Protein Data Bank Entry:

PDB ID : 1xwf

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 2004-11-01

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Adenosylhomocysteinase
ID:	SAHH_RAT
AC:	P10760
Organism:	Rattus norvegicus
Reign:	Eukaryota
TaxID:	10116
EC Number:	3.3.1.1

Chains:

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

Ligand binding site composition:

B-Factor:	19.320
Number of residues:	29
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:	NAD
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.863	870.750

% Hydrophobic	% Polar
47.29	52.71
According to VolSite

Ligand :

HET Code:	ADN
Formula:	C10H13N5O4
Molecular weight:	267.241 g/mol
DrugBank ID:	DB00640
Buried Surface Area:	73.34 %
Polar Surface area:	139.54 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	2

Mass center Coordinates

X	Y	Z
57.6012	33.8567	8.78037

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
O5'	NE2	HIS- 54	3.11	152.7	H-Bond (Ligand Donor)	false
N1	OG1	THR- 56	2.88	162.84	H-Bond (Protein Donor)	false
N6	OE2	GLU- 58	3.09	164.33	H-Bond (Ligand Donor)	false
O2'	OE1	GLU- 155	3.27	138.01	H-Bond (Ligand Donor)	false
O3'	OD1	ASP- 189	3.02	160.15	H-Bond (Ligand Donor)	false
O3'	OD2	ASP- 189	3.48	126.33	H-Bond (Ligand Donor)	false
C5'	CD2	LEU- 343	3.97	0	Hydrophobic	false
C5'	CD1	LEU- 346	4.33	0	Hydrophobic	false
N7	N	HIS- 352	3.02	171.5	H-Bond (Protein Donor)	false
N6	O	HIS- 352	3.38	134.84	H-Bond (Ligand Donor)	false
C2'	CE	MET- 357	3.97	0	Hydrophobic	false
C5'	C3N	NAD- 432	4.36	0	Hydrophobic	false
C3'	C4N	NAD- 432	4	0	Hydrophobic	false