scPDB - 5c3y entry

Protein Data Bank Entry:

PDB ID : 5c3y

Resolution :2.600 Å

Experimental Method : X-ray

Deposition Date : 2015-06-17

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Ribokinase
ID:	RBSK_HUMAN
AC:	Q9H477
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	50.850
Number of residues:	33
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	NA

Cavity properties

Ligandability	Volume (Å3)
0.724	526.500

% Hydrophobic	% Polar
47.44	52.56
According to VolSite

Ligand :

HET Code:	AN2
Formula:	C10H14N6O9P2
Molecular weight:	424.200 g/mol
DrugBank ID:	-
Buried Surface Area:	64.26 %
Polar Surface area:	263.66 Å2

Number of
H-Bond Acceptors:	13
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
39.7764	14.976	101.316

Binding mode :

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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
O1A	OG1	THR- 235	2.64	172.37	H-Bond (Protein Donor)	false
C5'	CB	THR- 235	3.98	0	Hydrophobic	false
O3'	O	GLY- 240	2.81	153.62	H-Bond (Ligand Donor)	false
C5'	CB	ALA- 267	4.32	0	Hydrophobic	false
O1B	N	GLY- 268	3.09	169.5	H-Bond (Protein Donor)	false
C4'	CB	PHE- 271	4.25	0	Hydrophobic	false
O2'	OD1	ASN- 295	2.82	155.51	H-Bond (Ligand Donor)	false
C4'	CB	ALA- 298	4.17	0	Hydrophobic	false
C1'	CB	ALA- 298	3.66	0	Hydrophobic	false