scPDB - 5ark entry

Protein Data Bank Entry:

PDB ID : 5ark

Resolution :2.280 Å

Experimental Method : X-ray

Deposition Date : 2015-09-25

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Ribonuclease 4
ID:	RNAS4_PIG
AC:	P15468
Organism:	Sus scrofa
Reign:	Eukaryota
TaxID:	9823
EC Number:	3.1.27

Chains:

Chain Name:	Percentage of Residues within binding site
B	71 %
C	29 %

Ligand binding site composition:

B-Factor:	40.122
Number of residues:	25
Including
Standard Amino Acids:	24
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.109	570.375

% Hydrophobic	% Polar
44.38	55.62
According to VolSite

Ligand :

HET Code:	UMP
Formula:	C9H11N2O8P
Molecular weight:	306.166 g/mol
DrugBank ID:	DB03800
Buried Surface Area:	67.01 %
Polar Surface area:	161.1 Å2

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

Mass center Coordinates

X	Y	Z
10.6104	-32.6581	-48.1302

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
OP2	NH2	ARG- 7	2.9	127.65	H-Bond (Protein Donor)	false
OP2	CZ	ARG- 7	3.09	0	Ionic (Protein Cationic)	false
OP2	NE2	GLN- 11	3.31	141.07	H-Bond (Protein Donor)	false
OP3	NE2	HIS- 12	3.32	135.33	H-Bond (Protein Donor)	false
C1'	CE1	PHE- 42	3.65	0	Hydrophobic	false
C2'	CD1	PHE- 42	3.92	0	Hydrophobic	false
C5'	CB	PHE- 117	3.78	0	Hydrophobic	false
C1'	CD2	PHE- 117	4.28	0	Hydrophobic	false
OP3	N	PHE- 117	2.84	170.55	H-Bond (Protein Donor)	false