scPDB - 1lwx entry

Protein Data Bank Entry:

PDB ID : 1lwx

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 1997-04-30

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, cytosolic
ID:	NDKC_DICDI
AC:	P22887
Organism:	Dictyostelium discoideum
Reign:	Eukaryota
TaxID:	44689
EC Number:	2.7.4.6

Chains:

Chain Name:	Percentage of Residues within binding site
A	4 %
C	96 %

Ligand binding site composition:

B-Factor:	27.796
Number of residues:	27
Including
Standard Amino Acids:	25
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.211	340.875

% Hydrophobic	% Polar
56.44	43.56
According to VolSite

Ligand :

HET Code:	AZD
Formula:	C10H12N5O10P2
Molecular weight:	424.177 g/mol
DrugBank ID:	DB04542
Buried Surface Area:	58.59 %
Polar Surface area:	249.78 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	1
Rings:	2
Aromatic rings:	0
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
51.9571	2.1747	10.1349

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
N4'	NZ	LYS- 16	3.25	138.99	H-Bond (Protein Donor)	false
N5'	OH	TYR- 56	3.46	127.31	H-Bond (Protein Donor)	false
C5'	CE1	TYR- 56	3.38	0	Hydrophobic	false
O1A	NE2	HIS- 59	3.13	152.52	H-Bond (Protein Donor)	false
C5A	CZ	PHE- 64	3.36	0	Hydrophobic	false
C1'	CD1	LEU- 68	3.65	0	Hydrophobic	false
C4'	CD2	LEU- 68	3.48	0	Hydrophobic	false
O1B	NH1	ARG- 92	2.98	151.93	H-Bond (Protein Donor)	false
O1B	NH2	ARG- 92	3.29	137.21	H-Bond (Protein Donor)	false
O2B	NH2	ARG- 92	3.01	157	H-Bond (Protein Donor)	false
O1B	CZ	ARG- 92	3.58	0	Ionic (Protein Cationic)	false
O2B	CZ	ARG- 92	3.92	0	Ionic (Protein Cationic)	false
O2B	OG1	THR- 98	3.19	164.92	H-Bond (Protein Donor)	false
C5A	CG2	THR- 98	4.18	0	Hydrophobic	false
O2B	CZ	ARG- 109	3.91	0	Ionic (Protein Cationic)	false
O3B	CZ	ARG- 109	3.75	0	Ionic (Protein Cationic)	false
O2B	NH1	ARG- 109	2.99	155.09	H-Bond (Protein Donor)	false
O3B	NH2	ARG- 109	2.93	172.48	H-Bond (Protein Donor)	false
C2'	CG1	VAL- 116	4.47	0	Hydrophobic	false
C2'	CB	ALA- 119	3.94	0	Hydrophobic	false
O1A	MG	MG- 157	2.78	0	Metal Acceptor	false
O1B	MG	MG- 157	2.62	0	Metal Acceptor	false