scPDB - 1st0 entry

Protein Data Bank Entry:

PDB ID : 1st0

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2004-03-24

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	m7GpppX diphosphatase
ID:	DCPS_HUMAN
AC:	Q96C86
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	3.6.1.59

Chains:

Chain Name:	Percentage of Residues within binding site
A	86 %
B	14 %

Ligand binding site composition:

B-Factor:	25.692
Number of residues:	50
Including
Standard Amino Acids:	50
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.500	1957.500

% Hydrophobic	% Polar
41.90	58.10
According to VolSite

Ligand :

HET Code:	GTG
Formula:	C21H27N10O18P3
Molecular weight:	800.417 g/mol
DrugBank ID:	DB03958
Buried Surface Area:	72.46 %
Polar Surface area:	447.71 Å2

Number of
H-Bond Acceptors:	23
H-Bond Donors:	8
Rings:	6
Aromatic rings:	2
Anionic atoms:	3
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	12

Mass center Coordinates

X	Y	Z
35.1615	57.0563	55.8143

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
O2E	NH2	ARG- 54	2.93	148.66	H-Bond (Protein Donor)	false
N2B	OD1	ASP- 59	3.04	139.95	H-Bond (Ligand Donor)	false
N1B	OE1	GLU- 85	3.47	132.43	H-Bond (Ligand Donor)	false
N1B	OE2	GLU- 85	2.61	156.63	H-Bond (Ligand Donor)	false
N2B	OE1	GLU- 85	2.83	167.46	H-Bond (Ligand Donor)	false
C7X	CE1	TYR- 113	3.35	0	Hydrophobic	false
O6B	NZ	LYS- 128	2.94	139.72	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 142	3.65	0	Ionic (Protein Cationic)	false
O2B	NZ	LYS- 142	3.39	0	Ionic (Protein Cationic)	false
O1G	NZ	LYS- 142	3.88	0	Ionic (Protein Cationic)	false
C7X	CE2	TRP- 175	3.65	0	Hydrophobic	false
C5D	CZ2	TRP- 175	4.44	0	Hydrophobic	false
DuAr	DuAr	TRP- 175	3.52	0	Aromatic Face/Face	false
N1A	OE2	GLU- 185	2.7	160.95	H-Bond (Ligand Donor)	false
N2A	OE1	GLU- 185	2.83	174.5	H-Bond (Ligand Donor)	false
N2A	OE2	GLU- 185	3.42	129.15	H-Bond (Ligand Donor)	false
N2A	O	PRO- 204	3.04	139.46	H-Bond (Ligand Donor)	false
O3D	OD2	ASP- 205	2.52	157.83	H-Bond (Ligand Donor)	false
O2D	OD1	ASP- 205	2.7	149.82	H-Bond (Ligand Donor)	false
O2D	OD2	ASP- 205	3.32	148.23	H-Bond (Ligand Donor)	false
C7X	CD1	LEU- 206	3.92	0	Hydrophobic	false
C2D	CB	LEU- 206	4.38	0	Hydrophobic	false
N3A	N	LEU- 206	3.24	148.23	H-Bond (Protein Donor)	false
O2D	NZ	LYS- 207	3.31	158.46	H-Bond (Protein Donor)	false
C4D	CD1	ILE- 219	3.79	0	Hydrophobic	false
O2A	N	SER- 272	2.87	132.51	H-Bond (Protein Donor)	false
O3A	N	SER- 272	3.27	160.12	H-Bond (Protein Donor)	false
O1B	OG	SER- 272	2.59	148.8	H-Bond (Protein Donor)	false
O2A	N	TYR- 273	2.96	162.92	H-Bond (Protein Donor)	false
C7X	CZ	TYR- 273	4.1	0	Hydrophobic	false
C5D	CD1	TYR- 273	3.73	0	Hydrophobic	false
O1A	NE2	HIS- 279	3.2	129.18	H-Bond (Protein Donor)	false
C4E	CB	PRO- 288	4.13	0	Hydrophobic	false
C1E	CB	PRO- 288	4.26	0	Hydrophobic	false
O3A	NH2	ARG- 294	3.26	130.47	H-Bond (Protein Donor)	false
O1B	NH1	ARG- 294	3.34	135.71	H-Bond (Protein Donor)	false
O1B	NH2	ARG- 294	2.91	160	H-Bond (Protein Donor)	false
O5E	NH1	ARG- 294	3.38	142.07	H-Bond (Protein Donor)	false
O1B	CZ	ARG- 294	3.55	0	Ionic (Protein Cationic)	false