scPDB - 4mvc entry

Protein Data Bank Entry:

PDB ID : 4mvc

Resolution :3.000 Å

Experimental Method : X-ray

Deposition Date : 2013-09-23

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Choline-phosphate cytidylyltransferase A
ID:	PCY1A_RAT
AC:	P19836
Organism:	Rattus norvegicus
Reign:	Eukaryota
TaxID:	10116
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	32.988
Number of residues:	39
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.599	877.500

% Hydrophobic	% Polar
41.15	58.85
According to VolSite

Ligand :

HET Code:	CDC
Formula:	C14H25N4O11P2
Molecular weight:	487.316 g/mol
DrugBank ID:	DB04290
Buried Surface Area:	75.46 %
Polar Surface area:	235.94 Å2

Number of
H-Bond Acceptors:	13
H-Bond Donors:	3
Rings:	2
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
8.82271	-14.9262	-32.685

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
N11	OD2	ASP- 82	3.44	0	Ionic (Ligand Cationic)	false
O1A	N	ILE- 84	3.18	123.85	H-Bond (Protein Donor)	false
O3A	N	ILE- 84	3.18	152.26	H-Bond (Protein Donor)	false
O1A	N	PHE- 85	2.93	167.44	H-Bond (Protein Donor)	false
C5'	CE1	PHE- 85	3.44	0	Hydrophobic	false
C1'	CB	ALA- 95	3.53	0	Hydrophobic	false
O2A	NZ	LYS- 122	3.57	0	Ionic (Protein Cationic)	false
O3B	NZ	LYS- 122	3.72	0	Ionic (Protein Cationic)	false
O2B	NE2	HIS- 168	2.71	165.5	H-Bond (Protein Donor)	false
O2'	OD2	ASP- 169	3.45	171.27	H-Bond (Ligand Donor)	false
O3B	OH	TYR- 173	3.16	138.11	H-Bond (Protein Donor)	false
C14	CE1	TYR- 173	3.64	0	Hydrophobic	false
N3	N	THR- 197	3.17	135.4	H-Bond (Protein Donor)	false
N4	O	THR- 197	3.38	169.89	H-Bond (Ligand Donor)	false
N4	O	ILE- 200	2.89	125.49	H-Bond (Ligand Donor)	false