scPDB - 2dy9 entry

Protein Data Bank Entry:

PDB ID : 2dy9

Resolution :2.010 Å

Experimental Method : X-ray

Deposition Date : 2006-09-08

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Nucleoside diphosphate kinase
ID:	NDK_PYRHO
AC:	O58429
Organism:	Pyrococcus horikoshii
Reign:	Archaea
TaxID:	70601
EC Number:	2.7.4.6

Chains:

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

Ligand binding site composition:

B-Factor:	16.289
Number of residues:	27
Including
Standard Amino Acids:	24
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.195	236.250

% Hydrophobic	% Polar
61.43	38.57
According to VolSite

Ligand :

HET Code:	ADP
Formula:	C10H12N5O10P2
Molecular weight:	424.177 g/mol
DrugBank ID:	-
Buried Surface Area:	58.07 %
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
19.4526	34.4735	44.4993

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
O2'	NZ	LYS- 15	3.19	131.09	H-Bond (Protein Donor)	false
C5'	CE1	TYR- 55	3.81	0	Hydrophobic	false
O1A	NE2	HIS- 58	3.21	147.04	H-Bond (Protein Donor)	false
C1'	CE1	PHE- 63	4.17	0	Hydrophobic	false
DuAr	DuAr	PHE- 63	3.75	0	Aromatic Face/Face	false
C5'	CD2	LEU- 67	4.34	0	Hydrophobic	false
C4'	CD1	LEU- 67	3.84	0	Hydrophobic	false
C1'	CD1	LEU- 67	3.8	0	Hydrophobic	false
O1B	CZ	ARG- 91	3.62	0	Ionic (Protein Cationic)	false
O1B	NH1	ARG- 91	2.84	171.61	H-Bond (Protein Donor)	false
O2B	OG1	THR- 97	2.64	164.43	H-Bond (Protein Donor)	false
C3'	CG2	THR- 97	3.49	0	Hydrophobic	false
O2B	NH1	ARG- 108	3.04	150.53	H-Bond (Protein Donor)	false
O3B	NH2	ARG- 108	3.23	139.66	H-Bond (Protein Donor)	false
O2B	CZ	ARG- 108	3.77	0	Ionic (Protein Cationic)	false
O2'	O	ILE- 119	2.97	144.76	H-Bond (Ligand Donor)	false
N3	N	ILE- 119	3.13	155.75	H-Bond (Protein Donor)	false
C2'	CB	ILE- 119	4.14	0	Hydrophobic	false
O1B	MG	MG- 601	2.48	0	Metal Acceptor	false
O1A	MG	MG- 601	2.29	0	Metal Acceptor	false
O3B	O	HOH- 714	2.85	179.98	H-Bond (Protein Donor)	false
O1B	O	HOH- 730	3.32	130.33	H-Bond (Protein Donor)	false