scPDB - 2npi entry

Protein Data Bank Entry:

PDB ID : 2npi

Resolution :2.950 Å

Experimental Method : X-ray

Deposition Date : 2006-10-27

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	mRNA cleavage and polyadenylation factor CLP1
ID:	CLP1_YEAST
AC:	Q08685
Organism:	Saccharomyces cerevisiae
Reign:	Eukaryota
TaxID:	559292
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	42.131
Number of residues:	41
Including
Standard Amino Acids:	39
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.936	833.625

% Hydrophobic	% Polar
42.11	57.89
According to VolSite

Ligand :

HET Code:	ATP
Formula:	C10H12N5O13P3
Molecular weight:	503.149 g/mol
DrugBank ID:	DB00171
Buried Surface Area:	71.54 %
Polar Surface area:	319.88 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
33.2885	38.0324	95.9719

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
N6	OD2	ASP- 33	3.43	144.72	H-Bond (Ligand Donor)	false
C2'	CZ	PHE- 56	4.17	0	Hydrophobic	false
O2'	O	LYS- 72	2.71	124.44	H-Bond (Ligand Donor)	false
O1G	NE2	GLN- 133	3.04	164.71	H-Bond (Protein Donor)	false
C5'	CG	GLN- 133	4.07	0	Hydrophobic	false
O2B	N	GLY- 135	2.53	149.02	H-Bond (Protein Donor)	false
O3G	NZ	LYS- 136	3.47	125.78	H-Bond (Protein Donor)	false
O2B	N	LYS- 136	2.9	127.72	H-Bond (Protein Donor)	false
O3G	NZ	LYS- 136	3.47	0	Ionic (Protein Cationic)	false
O1B	N	THR- 137	3.13	140.94	H-Bond (Protein Donor)	false
O2A	N	THR- 137	3.26	121.72	H-Bond (Protein Donor)	false
O2A	N	SER- 138	3.1	172.21	H-Bond (Protein Donor)	false
O2A	OG	SER- 138	2.85	152.71	H-Bond (Protein Donor)	false
C5'	CG1	VAL- 313	4.08	0	Hydrophobic	false
O4'	N	SER- 314	3.4	160.26	H-Bond (Protein Donor)	false
C4'	CG2	VAL- 316	4.09	0	Hydrophobic	false
O1G	NZ	LYS- 321	3.32	0	Ionic (Protein Cationic)	false
O2G	MG	MG- 2500	2.02	0	Metal Acceptor	false
O1B	MG	MG- 2500	2.48	0	Metal Acceptor	false