scPDB - 2v9x entry

Protein Data Bank Entry:

PDB ID : 2v9x

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2007-08-28

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	dCTP deaminase
ID:	DCD_ECOLI
AC:	P28248
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
G	32 %
H	68 %

Ligand binding site composition:

B-Factor:	24.028
Number of residues:	40
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.158	259.875

% Hydrophobic	% Polar
50.65	49.35
According to VolSite

Ligand :

HET Code:	DUT
Formula:	C9H11N2O14P3
Molecular weight:	464.110 g/mol
DrugBank ID:	DB02333
Buried Surface Area:	78.63 %
Polar Surface area:	279.44 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	2
Rings:	2
Aromatic rings:	0
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-53.6343	26.4428	136.243

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
O1B	CZ	ARG- 110	3.85	0	Ionic (Protein Cationic)	false
O2B	CZ	ARG- 110	3.64	0	Ionic (Protein Cationic)	false
O2B	NH2	ARG- 110	3.34	131.7	H-Bond (Protein Donor)	false
O2B	NE	ARG- 110	3.14	139.33	H-Bond (Protein Donor)	false
C5'	CB	SER- 111	4.38	0	Hydrophobic	false
O2A	N	SER- 111	2.86	169.24	H-Bond (Protein Donor)	false
O3A	N	SER- 111	3.44	127.31	H-Bond (Protein Donor)	false
O1B	OG	SER- 112	2.64	149.05	H-Bond (Protein Donor)	false
O1B	N	SER- 112	3.06	151.01	H-Bond (Protein Donor)	false
O1A	NH2	ARG- 126	2.99	128.6	H-Bond (Protein Donor)	false
C2'	CD1	ILE- 127	4.09	0	Hydrophobic	false
O3'	N	ASP- 128	3.1	156.5	H-Bond (Protein Donor)	false
O3'	OD2	ASP- 128	2.69	156.76	H-Bond (Ligand Donor)	false
C1'	CZ3	TRP- 131	3.74	0	Hydrophobic	false
C4'	CZ3	TRP- 131	3.78	0	Hydrophobic	false
C2'	CE3	TRP- 131	3.61	0	Hydrophobic	false
N3	O	VAL- 136	2.81	162.92	H-Bond (Ligand Donor)	false
O2	N	VAL- 136	3.01	154.01	H-Bond (Protein Donor)	false
C4'	CZ	TYR- 171	4	0	Hydrophobic	false
C5'	CE1	TYR- 171	3.92	0	Hydrophobic	false
O3G	CZ	ARG- 174	3.76	0	Ionic (Protein Cationic)	false
O3G	NH1	ARG- 174	3.01	172.72	H-Bond (Protein Donor)	false
O1G	NZ	LYS- 178	2.71	157.6	H-Bond (Protein Donor)	false
O2G	N	LYS- 178	2.96	177.91	H-Bond (Protein Donor)	false
O1G	NZ	LYS- 178	2.71	0	Ionic (Protein Cationic)	false
C5'	CD1	TYR- 179	4.19	0	Hydrophobic	false
O2	NE2	GLN- 182	3.05	150.73	H-Bond (Protein Donor)	false
O1A	MG	MG- 1195	2.07	0	Metal Acceptor	false
O2B	MG	MG- 1195	2.03	0	Metal Acceptor	false
O3G	MG	MG- 1195	2.08	0	Metal Acceptor	false
O2A	O	HOH- 2033	2.59	179.97	H-Bond (Protein Donor)	false