scPDB - 3elb entry

Protein Data Bank Entry:

PDB ID : 3elb

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2008-09-22

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Ethanolamine-phosphate cytidylyltransferase
ID:	PCY2_HUMAN
AC:	Q99447
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.7.7.14

Chains:

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

Ligand binding site composition:

B-Factor:	22.041
Number of residues:	35
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.763	583.875

% Hydrophobic	% Polar
45.66	54.34
According to VolSite

Ligand :

HET Code:	C5P
Formula:	C9H12N3O8P
Molecular weight:	321.181 g/mol
DrugBank ID:	DB03403
Buried Surface Area:	73.51 %
Polar Surface area:	190.61 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	3
Rings:	2
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
22.971	3.0379	54.1495

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
O3P	N	ALA- 221	2.8	151.1	H-Bond (Protein Donor)	false
O1P	N	PHE- 222	3	138.99	H-Bond (Protein Donor)	false
C5'	CZ	PHE- 222	3.69	0	Hydrophobic	false
O1P	NE2	HIS- 229	2.78	147.68	H-Bond (Protein Donor)	false
C1'	CG	PHE- 232	3.62	0	Hydrophobic	false
C4'	CE2	PHE- 232	3.86	0	Hydrophobic	false
O3P	NZ	LYS- 259	3.78	0	Ionic (Protein Cationic)	false
O2P	NZ	LYS- 259	3.1	0	Ionic (Protein Cationic)	false
O3'	N	GLY- 308	3.01	147.68	H-Bond (Protein Donor)	false
O2'	N	GLY- 308	2.87	122.13	H-Bond (Protein Donor)	false
C2'	CG2	THR- 310	4.21	0	Hydrophobic	false
O2'	OG1	THR- 310	2.83	167.01	H-Bond (Ligand Donor)	false
N3	OG	SER- 336	2.81	169.62	H-Bond (Protein Donor)	false
N4	O	SER- 338	2.9	151.55	H-Bond (Ligand Donor)	false
N4	O	LEU- 340	2.78	171.73	H-Bond (Ligand Donor)	false
O3'	O	HOH- 549	2.72	179.96	H-Bond (Protein Donor)	false
O2	O	HOH- 645	2.7	179.96	H-Bond (Protein Donor)	false