scPDB - 3otx entry

Protein Data Bank Entry:

PDB ID : 3otx

Resolution :1.550 Å

Experimental Method : X-ray

Deposition Date : 2010-09-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Adenosine kinase, putative
ID:	Q584S0_TRYB2
AC:	Q584S0
Organism:	Trypanosoma brucei brucei
Reign:	Eukaryota
TaxID:	185431
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	18.586
Number of residues:	70
Including
Standard Amino Acids:	64
Non Standard Amino Acids:	1
Water Molecules:	5
Cofactors:
Metals:	NA

Cavity properties

Ligandability	Volume (Å3)
0.396	2139.750

% Hydrophobic	% Polar
41.64	58.36
According to VolSite

Ligand :

HET Code:	AP5
Formula:	C20H24N10O22P5
Molecular weight:	911.327 g/mol
DrugBank ID:	DB01717
Buried Surface Area:	64.78 %
Polar Surface area:	543.69 Å2

Number of
H-Bond Acceptors:	30
H-Bond Donors:	6
Rings:	6
Aromatic rings:	4
Anionic atoms:	5
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	16

Mass center Coordinates

X	Y	Z
20.1179	4.6146	23.7282

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
N1B	ND2	ASN- 13	3.13	170.41	H-Bond (Protein Donor)	false
O3J	OD2	ASP- 17	2.63	168.85	H-Bond (Ligand Donor)	false
O2J	OD1	ASP- 17	2.63	173.82	H-Bond (Ligand Donor)	false
O3J	N	GLY- 63	3.4	133.75	H-Bond (Protein Donor)	false
O2J	N	GLY- 63	2.98	149.37	H-Bond (Protein Donor)	false
C1J	CB	SER- 64	4.32	0	Hydrophobic	false
N3B	N	SER- 64	3.04	166.37	H-Bond (Protein Donor)	false
O3J	ND2	ASN- 67	3.01	147.85	H-Bond (Protein Donor)	false
C2J	SG	CYS- 123	3.93	0	Hydrophobic	false
O1D	NH2	ARG- 132	3.07	171.99	H-Bond (Protein Donor)	false
O1D	CZ	ARG- 132	3.82	0	Ionic (Protein Cationic)	false
C5J	CD1	LEU- 134	4.06	0	Hydrophobic	false
DuAr	DuAr	PHE- 169	3.73	0	Aromatic Face/Face	false
O1B	ND2	ASN- 222	2.84	164.92	H-Bond (Protein Donor)	false
O2A	OG1	THR- 264	2.78	160.58	H-Bond (Protein Donor)	false
C5F	CB	THR- 264	3.88	0	Hydrophobic	false
C3F	CB	THR- 264	4.48	0	Hydrophobic	false
O2A	N	ASP- 266	2.99	159.75	H-Bond (Protein Donor)	false
C3F	CG2	VAL- 283	4.19	0	Hydrophobic	false
C2F	CG1	VAL- 283	3.72	0	Hydrophobic	false
N6A	OE1	GLN- 288	2.86	176.08	H-Bond (Ligand Donor)	false
N1A	NE2	GLN- 288	3.1	169.1	H-Bond (Protein Donor)	false
O1G	N	ALA- 297	3.03	157.07	H-Bond (Protein Donor)	false
C1F	CB	ALA- 297	4.44	0	Hydrophobic	false
C5F	CB	ALA- 297	3.8	0	Hydrophobic	false
O1E	N	ASP- 299	2.83	149.97	H-Bond (Protein Donor)	false
C5F	CB	PHE- 301	4.31	0	Hydrophobic	false
C4F	CB	ALA- 326	3.71	0	Hydrophobic	false
C1F	CB	ALA- 326	3.71	0	Hydrophobic	false
C1F	CG	GLN- 327	4.32	0	Hydrophobic	false
N3A	NE2	GLN- 327	3.16	165.03	H-Bond (Protein Donor)	false
O3F	O	HOH- 368	2.68	141.67	H-Bond (Protein Donor)	false
O4J	O	HOH- 638	3.13	179.97	H-Bond (Protein Donor)	false