scPDB - 1z4i entry

Protein Data Bank Entry:

PDB ID : 1z4i

Resolution :1.980 Å

Experimental Method : X-ray

Deposition Date : 2005-03-16

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	5'(3')-deoxyribonucleotidase, mitochondrial
ID:	NT5M_HUMAN
AC:	Q9NPB1
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	3.1.3

Chains:

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

Ligand binding site composition:

B-Factor:	25.710
Number of residues:	30
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.380	617.625

% Hydrophobic	% Polar
56.28	43.72
According to VolSite

Ligand :

HET Code:	UMP
Formula:	C9H11N2O8P
Molecular weight:	306.166 g/mol
DrugBank ID:	DB03800
Buried Surface Area:	73.5 %
Polar Surface area:	161.1 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	2
Rings:	2
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
12.8239	41.1997	27.1273

Binding mode :

What is Poseview ?

2D View
3D View

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
OP1	ND2	ASN- 41	2.9	157.35	H-Bond (Protein Donor)	false
OP3	ND2	ASN- 41	3.21	134.02	H-Bond (Protein Donor)	false
C5'	CB	ASP- 43	4.04	0	Hydrophobic	false
O5'	OD2	ASP- 43	2.76	165.3	H-Bond (Protein Donor)	false
OP2	N	ASP- 43	2.75	171.35	H-Bond (Protein Donor)	false
C2'	CE2	PHE- 49	3.83	0	Hydrophobic	false
C5'	CZ	PHE- 75	4.12	0	Hydrophobic	false
O4	N	SER- 78	3.23	176.55	H-Bond (Protein Donor)	false
O4	OG	SER- 78	3.42	146.16	H-Bond (Protein Donor)	false
C2'	CZ	PHE- 102	4.38	0	Hydrophobic	false
C3'	CE1	PHE- 102	4.36	0	Hydrophobic	false
OP2	OG1	THR- 130	2.64	163.86	H-Bond (Protein Donor)	false
O3'	O	SER- 131	2.76	177.5	H-Bond (Ligand Donor)	false
OP1	N	SER- 131	3.04	164.9	H-Bond (Protein Donor)	false
C2'	CG2	ILE- 133	3.54	0	Hydrophobic	false
OP2	NZ	LYS- 143	3.52	0	Ionic (Protein Cationic)	false
OP3	MG	MG- 1228	2.13	0	Metal Acceptor	false