scPDB - 3rw9 entry

Protein Data Bank Entry:

PDB ID : 3rw9

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2011-05-08

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Spermidine synthase
ID:	SPEE_HUMAN
AC:	P19623
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.5.1.16

Chains:

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

Ligand binding site composition:

B-Factor:	24.627
Number of residues:	37
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.860	772.875

% Hydrophobic	% Polar
48.47	51.53
According to VolSite

Ligand :

HET Code:	DSH
Formula:	C13H21N6O3S
Molecular weight:	341.409 g/mol
DrugBank ID:	-
Buried Surface Area:	78.63 %
Polar Surface area:	172.25 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
2.90665	65.9048	7.91965

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
O2'	NE2	GLN- 49	3.02	145.26	H-Bond (Protein Donor)	false
SD	CD1	LEU- 65	4.18	0	Hydrophobic	false
C3'	CD1	LEU- 65	3.87	0	Hydrophobic	false
SD	CB	GLN- 70	4.08	0	Hydrophobic	false
N	OE1	GLN- 80	3.29	145.81	H-Bond (Ligand Donor)	false
O3'	N	GLY- 103	3.37	134.81	H-Bond (Protein Donor)	false
O3'	OE1	GLU- 124	2.61	155.07	H-Bond (Ligand Donor)	false
O3'	OE2	GLU- 124	3.36	141.73	H-Bond (Ligand Donor)	false
N3	N	ILE- 125	3.33	130.11	H-Bond (Protein Donor)	false
C1'	CG2	ILE- 125	4.45	0	Hydrophobic	false
C3'	CG1	VAL- 129	4.44	0	Hydrophobic	false
N6	OD1	ASP- 155	2.7	163.02	H-Bond (Ligand Donor)	false
N1	N	GLY- 156	2.89	169.73	H-Bond (Protein Donor)	false
N6	O	PRO- 180	2.98	159.89	H-Bond (Ligand Donor)	false