scPDB - 2hxd entry

Protein Data Bank Entry:

PDB ID : 2hxd

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2006-08-03

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	dCTP deaminase, dUMP-forming
ID:	DCD_METJA
AC:	Q57872
Organism:	Methanocaldococcus jannaschii
Reign:	Archaea
TaxID:	243232
EC Number:	3.5.4.30

Chains:

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

Ligand binding site composition:

B-Factor:	32.177
Number of residues:	29
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.809	425.250

% Hydrophobic	% Polar
46.83	53.17
According to VolSite

Ligand :

HET Code:	DUP
Formula:	C9H12N3O13P3
Molecular weight:	463.125 g/mol
DrugBank ID:	DB01965
Buried Surface Area:	58.65 %
Polar Surface area:	282.23 Å2

Number of
H-Bond Acceptors:	13
H-Bond Donors:	3
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
45.4617	55.2029	105.846

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
O4	N	GLY- 132	2.88	145.48	H-Bond (Protein Donor)	false
C2'	CG2	ILE- 134	3.85	0	Hydrophobic	false
O3'	N	ASP- 135	3.21	162.05	H-Bond (Protein Donor)	false
O3'	OD1	ASP- 135	2.6	142.72	H-Bond (Ligand Donor)	false
C3'	CD1	PHE- 138	3.92	0	Hydrophobic	false
C4'	CE1	PHE- 138	4.15	0	Hydrophobic	false
C2'	CE1	PHE- 138	3.69	0	Hydrophobic	false
N3	O	THR- 143	2.97	176.68	H-Bond (Ligand Donor)	false
O2	N	THR- 143	2.85	160.79	H-Bond (Protein Donor)	false
C4'	CZ	TYR- 177	3.84	0	Hydrophobic	false
C5'	CE1	TYR- 177	3.77	0	Hydrophobic	false
O2G	OH	TYR- 177	2.52	145.55	H-Bond (Protein Donor)	false
O2G	N	LYS- 184	2.92	167.72	H-Bond (Protein Donor)	false
O3G	NZ	LYS- 184	2.78	166.58	H-Bond (Protein Donor)	false
O3G	NZ	LYS- 184	2.78	0	Ionic (Protein Cationic)	false
C5'	CD1	TYR- 185	4.01	0	Hydrophobic	false
O2	NE2	GLN- 188	3.19	155.27	H-Bond (Protein Donor)	false
O1A	MG	MG- 205	2.17	0	Metal Acceptor	false
O1B	MG	MG- 205	2.38	0	Metal Acceptor	false
O1G	MG	MG- 205	2.23	0	Metal Acceptor	false