scPDB - 3aca entry

Protein Data Bank Entry:

PDB ID : 3aca

Resolution :2.050 Å

Experimental Method : X-ray

Deposition Date : 2009-12-30

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	ADP-sugar pyrophosphatase
ID:	NUDT5_HUMAN
AC:	Q9UKK9
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	3.6.1.13

Chains:

Chain Name:	Percentage of Residues within binding site
A	27 %
B	73 %

Ligand binding site composition:

B-Factor:	37.338
Number of residues:	22
Including
Standard Amino Acids:	20
Non Standard Amino Acids:	2
Water Molecules:	0
Cofactors:
Metals:	MN MN

Cavity properties

Ligandability	Volume (Å3)
0.463	870.750

% Hydrophobic	% Polar
44.19	55.81
According to VolSite

Ligand :

HET Code:	8DD
Formula:	C10H12N5O10P2
Molecular weight:	424.177 g/mol
DrugBank ID:	-
Buried Surface Area:	59.32 %
Polar Surface area:	255 Å2

Number of
H-Bond Acceptors:	13
H-Bond Donors:	3
Rings:	3
Aromatic rings:	1
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
-22.17	19.787	75.7454

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
O2A	MN	MN- 1	2.63	0	Metal Acceptor	false
O2B	MN	MN- 1	2.52	0	Metal Acceptor	false
O2B	MN	MN- 2	2.37	0	Metal Acceptor	false
C5	CB	TRP- 28	4.16	0	Hydrophobic	false
C1'	CE3	TRP- 28	4.37	0	Hydrophobic	false
C5	CD2	TRP- 28	3.47	0	Hydrophobic	false
C1'	CZ2	TRP- 46	4.13	0	Hydrophobic	false
C4'	CZ2	TRP- 46	4.22	0	Hydrophobic	false
C5'	CH2	TRP- 46	3.84	0	Hydrophobic	false
DuAr	DuAr	TRP- 46	3.67	0	Aromatic Face/Face	false
N1	N	GLU- 47	2.89	167.32	H-Bond (Protein Donor)	false
N3	NH1	ARG- 51	3.17	158.78	H-Bond (Protein Donor)	false
O2A	NH2	ARG- 84	3.01	164.06	H-Bond (Protein Donor)	false
O5'	NH1	ARG- 84	3.36	129.93	H-Bond (Protein Donor)	false
O2A	CZ	ARG- 84	3.8	0	Ionic (Protein Cationic)	false
O1B	N	LEU- 98	3.43	144.59	H-Bond (Protein Donor)	false
C2'	CD1	LEU- 98	4.28	0	Hydrophobic	false
C3'	CD2	LEU- 98	4.08	0	Hydrophobic	false