scPDB - 4fyh entry

Protein Data Bank Entry:

PDB ID : 4fyh

Resolution :2.440 Å

Experimental Method : X-ray

Deposition Date : 2012-07-04

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
C	75 %
D	25 %

Ligand binding site composition:

B-Factor:	23.057
Number of residues:	30
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.732	529.875

% Hydrophobic	% Polar
52.23	47.77
According to VolSite

Ligand :

HET Code:	TR5
Formula:	C13H16N6O7P
Molecular weight:	399.276 g/mol
DrugBank ID:	-
Buried Surface Area:	62.72 %
Polar Surface area:	205.86 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	4
Rings:	4
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
12.8474	16.2186	45.2745

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
O3'	N	GLY- 16	2.88	152.45	H-Bond (Protein Donor)	false
O1	N	ILE- 18	2.82	176.92	H-Bond (Protein Donor)	false
C5'	CG1	ILE- 18	4.12	0	Hydrophobic	false
C5	CD1	ILE- 18	3.81	0	Hydrophobic	false
C2'	CD1	ILE- 18	3.81	0	Hydrophobic	false
O3	N	ARG- 19	2.86	162.83	H-Bond (Protein Donor)	false
O1	N	GLY- 20	3.23	155.85	H-Bond (Protein Donor)	false
C5	CG2	ILE- 65	4.04	0	Hydrophobic	false
C62	CD1	ILE- 65	3.73	0	Hydrophobic	false
N3	ND2	ASN- 69	3.41	169.86	H-Bond (Protein Donor)	false
O1	OG	SER- 87	2.58	148.45	H-Bond (Protein Donor)	false
O2	N	GLY- 89	2.86	143.61	H-Bond (Protein Donor)	false
C5'	CG2	VAL- 90	4.18	0	Hydrophobic	false
O3'	OE2	GLU- 93	2.76	163.75	H-Bond (Ligand Donor)	false
O3'	OE1	GLU- 93	3.48	125.59	H-Bond (Protein Donor)	false
O2	OG	SER- 117	2.71	130.68	H-Bond (Protein Donor)	false
C5	CB	ALA- 118	4.35	0	Hydrophobic	false
C1'	CG	MET- 119	3.65	0	Hydrophobic	false
N73	O	HOH- 306	3.49	142.32	H-Bond (Ligand Donor)	false