scPDB - 4a6a entry

Protein Data Bank Entry:

PDB ID : 4a6a

Resolution :2.900 Å

Experimental Method : X-ray

Deposition Date : 2011-11-01

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_MYCTU
AC:	P9WP17
Organism:	Mycobacterium tuberculosis
Reign:	Bacteria
TaxID:	83332
EC Number:	3.5.4.13

Chains:

Chain Name:	Percentage of Residues within binding site
A	69 %
E	31 %

Ligand binding site composition:

B-Factor:	46.663
Number of residues:	36
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.041	577.125

% Hydrophobic	% Polar
38.60	61.40
According to VolSite

Ligand :

HET Code:	TTP
Formula:	C10H13N2O14P3
Molecular weight:	478.137 g/mol
DrugBank ID:	DB02452
Buried Surface Area:	79.6 %
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
14.0446	-23.1237	36.9599

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
O1B	NZ	LYS- 101	3.6	0	Ionic (Protein Cationic)	false
O2B	NZ	LYS- 101	3.16	0	Ionic (Protein Cationic)	false
O2B	NZ	LYS- 101	3.16	173.84	H-Bond (Protein Donor)	false
O2A	N	SER- 102	3.14	176.08	H-Bond (Protein Donor)	false
O3A	N	SER- 102	3.4	122.55	H-Bond (Protein Donor)	false
C5'	CB	SER- 102	4.15	0	Hydrophobic	false
O1B	OG	SER- 103	2.9	149.94	H-Bond (Protein Donor)	false
O1B	N	SER- 103	3.18	157.43	H-Bond (Protein Donor)	false
C5M	CB	VAL- 115	3.75	0	Hydrophobic	false
C5M	CD1	ILE- 118	4.14	0	Hydrophobic	false
C2'	CD1	ILE- 118	3.74	0	Hydrophobic	false
O3'	N	ASP- 119	3.02	169.83	H-Bond (Protein Donor)	false
O3'	OD1	ASP- 119	3.07	165.82	H-Bond (Ligand Donor)	false
C1'	CE2	PHE- 122	3.77	0	Hydrophobic	false
C2'	CD2	PHE- 122	3.66	0	Hydrophobic	false
O2	N	THR- 127	3.15	168.93	H-Bond (Protein Donor)	false
N3	O	THR- 127	2.78	151.08	H-Bond (Ligand Donor)	false
O2A	NE2	GLN- 148	2.82	128.22	H-Bond (Protein Donor)	false
O3G	OH	TYR- 162	2.6	143.34	H-Bond (Protein Donor)	false
C5'	CE1	TYR- 162	3.83	0	Hydrophobic	false
C4'	CZ	TYR- 162	3.96	0	Hydrophobic	false
O1G	NZ	LYS- 170	2.82	170.82	H-Bond (Protein Donor)	false
O3G	N	LYS- 170	3.02	174.28	H-Bond (Protein Donor)	false
O1G	NZ	LYS- 170	2.82	0	Ionic (Protein Cationic)	false
C5'	CD2	TYR- 171	4	0	Hydrophobic	false
O2	NE2	GLN- 174	2.9	135.08	H-Bond (Protein Donor)	false
O1A	MG	MG- 202	2.5	0	Metal Acceptor	false
O2B	MG	MG- 202	2.27	0	Metal Acceptor	false
O2G	MG	MG- 202	2.59	0	Metal Acceptor	false