scPDB - 3bl7 entry

Protein Data Bank Entry:

PDB ID : 3bl7

Resolution :2.310 Å

Experimental Method : X-ray

Deposition Date : 2007-12-10

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	79 %
B	21 %

Ligand binding site composition:

B-Factor:	15.287
Number of residues:	30
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.206	2554.875

% Hydrophobic	% Polar
41.48	58.52
According to VolSite

Ligand :

HET Code:	DD1
Formula:	C21H25FN5O
Molecular weight:	382.454 g/mol
DrugBank ID:	DB07642
Buried Surface Area:	65.45 %
Polar Surface area:	91.49 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	3
Rings:	4
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
4.83482	0.307036	21.447

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
C36	CB	ASN- 110	3.82	0	Hydrophobic	false
C28	CE2	TYR- 113	3.79	0	Hydrophobic	false
C35	CB	TYR- 113	3.72	0	Hydrophobic	false
C34	CD1	TYR- 113	3.43	0	Hydrophobic	false
F58	CD	LYS- 142	4.25	0	Hydrophobic	false
C6	CG	LYS- 142	3.75	0	Hydrophobic	false
C5	CD2	TYR- 143	3.35	0	Hydrophobic	false
C28	CE2	TRP- 175	4.15	0	Hydrophobic	false
C35	CB	TRP- 175	3.66	0	Hydrophobic	false
DuAr	DuAr	TRP- 175	3.99	0	Aromatic Face/Face	false
DuAr	DuAr	TRP- 175	3.55	0	Aromatic Face/Face	false
N56	OE2	GLU- 185	3.07	156.84	H-Bond (Ligand Donor)	false
N48	OE1	GLU- 185	2.73	160.06	H-Bond (Ligand Donor)	false
N48	OE2	GLU- 185	3.38	140.18	H-Bond (Ligand Donor)	false
N56	O	PRO- 204	2.68	130.19	H-Bond (Ligand Donor)	false
N54	OD2	ASP- 205	3.1	167.44	H-Bond (Ligand Donor)	false
C28	CD2	LEU- 206	4.25	0	Hydrophobic	false
C38	CB	LEU- 206	3.74	0	Hydrophobic	false
C32	CD2	LEU- 206	3.78	0	Hydrophobic	false
N46	N	LEU- 206	3.19	136.08	H-Bond (Protein Donor)	false
F58	CB	SER- 272	3.44	0	Hydrophobic	false