scPDB - 1yc2 entry

Protein Data Bank Entry:

PDB ID : 1yc2

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2004-12-21

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	NAD-dependent protein deacylase 2
ID:	NPD2_ARCFU
AC:	O30124
Organism:	Archaeoglobus fulgidus
Reign:	Archaea
TaxID:	224325
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	52.447
Number of residues:	43
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.609	610.875

% Hydrophobic	% Polar
49.72	50.28
According to VolSite

Ligand :

HET Code:	APR
Formula:	C15H21N5O14P2
Molecular weight:	557.300 g/mol
DrugBank ID:	-
Buried Surface Area:	73.72 %
Polar Surface area:	316.8 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	6
Rings:	4
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
-34.4956	7.34706	-4.75336

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
O2B	N	ALA- 24	2.79	159.47	H-Bond (Protein Donor)	false
N6	OE1	GLU- 29	3.13	166.23	H-Bond (Ligand Donor)	false
C5'	CG2	THR- 34	4.23	0	Hydrophobic	false
O2A	N	PHE- 35	2.81	133.77	H-Bond (Protein Donor)	false
C1D	CG	PHE- 35	4.17	0	Hydrophobic	false
C2D	CZ	PHE- 35	4.2	0	Hydrophobic	false
C3D	CE2	PHE- 35	3.69	0	Hydrophobic	false
C5D	CD2	PHE- 35	3.4	0	Hydrophobic	false
O1A	NH2	ARG- 36	3.12	146.67	H-Bond (Protein Donor)	false
O2A	N	ARG- 36	2.71	170.29	H-Bond (Protein Donor)	false
O4D	NH1	ARG- 36	3.35	146.81	H-Bond (Protein Donor)	false
O4D	NH2	ARG- 36	3.2	155.91	H-Bond (Protein Donor)	false
O1D	NE1	TRP- 42	3.26	152.08	H-Bond (Protein Donor)	false
C1D	CZ2	TRP- 42	4.31	0	Hydrophobic	false
O3D	ND1	HIS- 118	2.66	140.16	H-Bond (Protein Donor)	false
O1B	OG	SER- 192	2.73	161.75	H-Bond (Protein Donor)	false
O5'	N	SER- 193	3.26	125.19	H-Bond (Protein Donor)	false
O1B	N	SER- 193	3.19	142.25	H-Bond (Protein Donor)	false
C4D	CG1	VAL- 196	4	0	Hydrophobic	false
O3'	ND2	ASN- 217	3.07	170.43	H-Bond (Protein Donor)	false
N3	N	ALA- 218	3.24	154.83	H-Bond (Protein Donor)	false
C1'	CB	ALA- 218	4.1	0	Hydrophobic	false
C2'	CG	GLU- 219	4.3	0	Hydrophobic	false
O2'	OE1	GLU- 219	2.8	161.46	H-Bond (Ligand Donor)	false
O3'	OE1	GLU- 219	3.32	161.79	H-Bond (Ligand Donor)	false
N1	N	ALA- 235	2.87	161.99	H-Bond (Protein Donor)	false