scPDB - 1rkd entry

Protein Data Bank Entry:

PDB ID : 1rkd

Resolution :1.840 Å

Experimental Method : X-ray

Deposition Date : 1997-11-29

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_ECOLI
AC:	P0A9J6
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	30.326
Number of residues:	39
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.208	361.125

% Hydrophobic	% Polar
61.68	38.32
According to VolSite

Ligand :

HET Code:	ADP
Formula:	C10H12N5O10P2
Molecular weight:	424.177 g/mol
DrugBank ID:	-
Buried Surface Area:	51.44 %
Polar Surface area:	260.7 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
-33.1608	17.578	46.1066

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
O2B	ND2	ASN- 187	3.05	170.49	H-Bond (Protein Donor)	false
O2A	OG1	THR- 223	2.94	157.89	H-Bond (Protein Donor)	false
C5'	CB	THR- 223	4.11	0	Hydrophobic	false
O2A	N	GLY- 225	2.85	144.07	H-Bond (Protein Donor)	false
O3'	O	GLY- 228	3.43	131.63	H-Bond (Ligand Donor)	false
C1'	CB	ALA- 253	4.27	0	Hydrophobic	false
C5'	CB	ALA- 253	4.4	0	Hydrophobic	false
O1B	N	GLY- 254	3.49	131.79	H-Bond (Protein Donor)	false
C4'	CB	PHE- 257	4.28	0	Hydrophobic	false
O2'	ND1	HIS- 279	2.86	148.78	H-Bond (Protein Donor)	false
C4'	CB	ALA- 282	4.4	0	Hydrophobic	false
C1'	CB	ALA- 282	3.73	0	Hydrophobic	false
N3	O	HOH- 393	3	179.96	H-Bond (Protein Donor)	false