scPDB - 4qak entry

Protein Data Bank Entry:

PDB ID : 4qak

Resolution :2.020 Å

Experimental Method : X-ray

Deposition Date : 2014-05-05

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	RNA 2',3'-cyclic phosphodiesterase
ID:	THPR_ECOLI
AC:	P37025
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	18 %
B	82 %

Ligand binding site composition:

B-Factor:	19.979
Number of residues:	24
Including
Standard Amino Acids:	22
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.702	1670.625

% Hydrophobic	% Polar
36.97	63.03
According to VolSite

Ligand :

HET Code:	2AM
Formula:	C10H12N5O7P
Molecular weight:	345.205 g/mol
DrugBank ID:	-
Buried Surface Area:	57.77 %
Polar Surface area:	201.54 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
30.0876	21.1369	21.4486

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
C5'	CE1	PHE- 8	3.79	0	Hydrophobic	false
C4'	CG	PHE- 8	4.29	0	Hydrophobic	false
O3'	NE2	HIS- 43	2.83	149.53	H-Bond (Ligand Donor)	false
C1'	CG2	THR- 45	4.24	0	Hydrophobic	false
C1'	CD1	PHE- 48	4.12	0	Hydrophobic	false
DuAr	DuAr	PHE- 48	3.34	0	Aromatic Face/Face	false
O3P	NH2	ARG- 86	2.86	166.93	H-Bond (Protein Donor)	false
O3P	CZ	ARG- 86	3.79	0	Ionic (Protein Cationic)	false
DuAr	CZ	ARG- 86	3.53	15.42	Pi/Cation	false
O1P	NE2	HIS- 125	2.63	168.03	H-Bond (Protein Donor)	false
O1P	OG1	THR- 127	3.27	129.21	H-Bond (Protein Donor)	false
O2P	OG1	THR- 127	2.85	161.09	H-Bond (Protein Donor)	false
O2P	CZ	ARG- 130	3.58	0	Ionic (Protein Cationic)	false
O3P	CZ	ARG- 130	3.64	0	Ionic (Protein Cationic)	false
O2P	NH2	ARG- 130	2.78	150.99	H-Bond (Protein Donor)	false
O3P	NH1	ARG- 130	2.8	171.93	H-Bond (Protein Donor)	false
N6	OD1	ASP- 131	2.68	142.13	H-Bond (Ligand Donor)	false
C5'	CE1	TYR- 166	4.13	0	Hydrophobic	false