scPDB - 4yv2 entry

Protein Data Bank Entry:

PDB ID : 4yv2

Resolution :2.170 Å

Experimental Method : X-ray

Deposition Date : 2015-03-19

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Spermidine synthase, putative
ID:	Q4DA73_TRYCC
AC:	Q4DA73
Organism:	Trypanosoma cruzi
Reign:	Eukaryota
TaxID:	353153
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	36.558
Number of residues:	30
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.322	435.375

% Hydrophobic	% Polar
45.74	54.26
According to VolSite

Ligand :

HET Code:	S4M
Formula:	C14H25N6O3S
Molecular weight:	357.452 g/mol
DrugBank ID:	-
Buried Surface Area:	69.64 %
Polar Surface area:	151.15 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	5
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
17.9421	18.1485	30.4573

Binding mode :

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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- 40	2.82	147.57	H-Bond (Protein Donor)	false
CE	SD	MET- 57	4.46	0	Hydrophobic	false
CE	CD1	LEU- 59	3.76	0	Hydrophobic	false
C5'	CD1	LEU- 59	4.46	0	Hydrophobic	false
C3'	CD1	LEU- 59	3.74	0	Hydrophobic	false
CB	CB	GLN- 64	3.98	0	Hydrophobic	false
CB	CG2	VAL- 65	4.07	0	Hydrophobic	false
N	NE2	HIS- 74	2.8	139.21	H-Bond (Ligand Donor)	false
N	OD2	ASP- 98	2.88	141.29	H-Bond (Ligand Donor)	false
N	OD2	ASP- 98	2.88	0	Ionic (Ligand Cationic)	false
N	OD1	ASP- 98	3.75	0	Ionic (Ligand Cationic)	false
O2'	OD1	ASP- 118	2.8	148.03	H-Bond (Ligand Donor)	false
O3'	OD2	ASP- 118	2.96	165.13	H-Bond (Ligand Donor)	false
O3'	OD1	ASP- 118	3.5	135.72	H-Bond (Ligand Donor)	false
N3	N	ILE- 119	3.29	149.59	H-Bond (Protein Donor)	false
C1'	CG2	ILE- 119	4.42	0	Hydrophobic	false
N6	OD1	ASP- 149	3.14	154.06	H-Bond (Ligand Donor)	false
N1	N	GLY- 150	2.89	163.96	H-Bond (Protein Donor)	false
N	OD1	ASP- 168	3.66	0	Ionic (Ligand Cationic)	false
N	OD2	ASP- 168	3.18	0	Ionic (Ligand Cationic)	false
N	OD2	ASP- 168	3.18	155.6	H-Bond (Ligand Donor)	false