scPDB - 4kxl entry

Protein Data Bank Entry:

PDB ID : 4kxl

Resolution :1.690 Å

Experimental Method : X-ray

Deposition Date : 2013-05-27

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	2'-deoxynucleoside 5'-phosphate N-hydrolase 1
ID:	DNPH1_RAT
AC:	O35820
Organism:	Rattus norvegicus
Reign:	Eukaryota
TaxID:	10116
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
B	3 %
C	19 %
D	77 %

Ligand binding site composition:

B-Factor:	10.889
Number of residues:	32
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.703	482.625

% Hydrophobic	% Polar
48.95	51.05
According to VolSite

Ligand :

HET Code:	6C6
Formula:	C15H20N5O7P
Molecular weight:	413.322 g/mol
DrugBank ID:	-
Buried Surface Area:	72.57 %
Polar Surface area:	187.55 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	3
Rings:	4
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
3.27611	-1.17529	37.0687

Binding mode :

What is Poseview ?

2D View
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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
O3'	N	GLY- 16	3.05	158.41	H-Bond (Protein Donor)	false
C5'	CG1	ILE- 18	3.92	0	Hydrophobic	false
C62	CG2	ILE- 18	3.83	0	Hydrophobic	false
C2'	CD1	ILE- 18	3.9	0	Hydrophobic	false
OA1	N	ILE- 18	2.79	161.77	H-Bond (Protein Donor)	false
OA3	N	ARG- 19	2.71	161.02	H-Bond (Protein Donor)	false
OA1	N	GLY- 20	3.05	157.87	H-Bond (Protein Donor)	false
O2'	NE2	HIS- 45	3.37	151.74	H-Bond (Protein Donor)	false
C2'	CG2	VAL- 46	3.69	0	Hydrophobic	false
C64	CG	GLU- 57	3.44	0	Hydrophobic	false
C65	CD1	ILE- 65	3.5	0	Hydrophobic	false
N3	ND2	ASN- 69	3.12	175.9	H-Bond (Protein Donor)	false
OA1	OG	SER- 87	2.72	158.21	H-Bond (Protein Donor)	false
OA2	N	GLY- 89	2.94	138.47	H-Bond (Protein Donor)	false
C4'	CG2	VAL- 90	4.08	0	Hydrophobic	false
O2'	OE1	GLU- 93	2.66	151.25	H-Bond (Ligand Donor)	false
O3'	OE2	GLU- 93	2.72	158.56	H-Bond (Ligand Donor)	false
OA2	OG	SER- 117	2.63	143.76	H-Bond (Protein Donor)	false
C61	CB	ALA- 118	3.89	0	Hydrophobic	false
C1'	CG	MET- 119	3.59	0	Hydrophobic	false