scPDB - 5c3z entry

Protein Data Bank Entry:

PDB ID : 5c3z

Resolution :1.900 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
B	100 %

Ligand binding site composition:

B-Factor:	38.871
Number of residues:	36
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	NA

Cavity properties

Ligandability	Volume (Å3)
0.534	499.500

% Hydrophobic	% Polar
47.30	52.70
According to VolSite

Ligand :

HET Code:	ACP
Formula:	C11H14N5O12P3
Molecular weight:	501.176 g/mol
DrugBank ID:	DB03909
Buried Surface Area:	62.1 %
Polar Surface area:	310.64 Å2

Number of
H-Bond Acceptors:	16
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
4.44032	34.6978	19.2753

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
O2A	OG1	THR- 235	2.67	157.87	H-Bond (Protein Donor)	false
C5'	CB	THR- 235	3.94	0	Hydrophobic	false
C3'	CB	THR- 235	4.37	0	Hydrophobic	false
C2'	CG2	THR- 256	4.35	0	Hydrophobic	false
O1G	OG1	THR- 264	2.79	163.7	H-Bond (Protein Donor)	false
C3B	CB	THR- 264	4.16	0	Hydrophobic	false
C5'	CB	ALA- 267	4.23	0	Hydrophobic	false
O1B	N	GLY- 268	2.88	153.92	H-Bond (Protein Donor)	false
C4'	CB	PHE- 271	4.17	0	Hydrophobic	false
O3'	OD1	ASN- 295	3.31	161.45	H-Bond (Ligand Donor)	false
O2'	OD1	ASN- 295	2.75	132.11	H-Bond (Ligand Donor)	false
C4'	CB	ALA- 298	3.83	0	Hydrophobic	false
C1'	CB	ALA- 298	3.64	0	Hydrophobic	false
O1A	O	HOH- 595	3.31	157.21	H-Bond (Protein Donor)	false