scPDB - 1xjk entry

Protein Data Bank Entry:

PDB ID : 1xjk

Resolution :2.120 Å

Experimental Method : X-ray

Deposition Date : 2004-09-23

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Vitamin B12-dependent ribonucleotide reductase
ID:	O33839_THEMT
AC:	O33839
Organism:	Thermotoga maritima
Reign:	Bacteria
TaxID:	2336
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	34 %
B	66 %

Ligand binding site composition:

B-Factor:	43.876
Number of residues:	39
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.573	631.125

% Hydrophobic	% Polar
46.52	53.48
According to VolSite

Ligand :

HET Code:	DGT
Formula:	C10H12N5O13P3
Molecular weight:	503.149 g/mol
DrugBank ID:	DB02181
Buried Surface Area:	67.53 %
Polar Surface area:	315.33 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	3
Rings:	3
Aromatic rings:	1
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-77.2409	-64.7055	-13.5722

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
O3'	OD1	ASP- 141	2.72	154.78	H-Bond (Ligand Donor)	false
O2A	N	ILE- 143	3.06	171.57	H-Bond (Protein Donor)	false
C2'	CG1	ILE- 143	3.85	0	Hydrophobic	false
C2'	CD1	ILE- 146	4.05	0	Hydrophobic	false
O1B	NZ	LYS- 158	2.87	149.09	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 158	3.1	155.96	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 158	2.87	0	Ionic (Protein Cationic)	false
O2A	NZ	LYS- 158	3.1	0	Ionic (Protein Cationic)	false
O1G	NH1	ARG- 171	2.9	155.47	H-Bond (Protein Donor)	false
O2G	NH1	ARG- 171	3.38	136.62	H-Bond (Protein Donor)	false
O2G	NH2	ARG- 171	3.24	141.23	H-Bond (Protein Donor)	false
O1G	CZ	ARG- 171	3.94	0	Ionic (Protein Cationic)	false
O2G	CZ	ARG- 171	3.73	0	Ionic (Protein Cationic)	false
C4'	CD	ARG- 171	3.78	0	Hydrophobic	false
C1'	CG2	VAL- 177	4.24	0	Hydrophobic	false
O1G	N	ALA- 178	3.14	169.96	H-Bond (Protein Donor)	false
C1'	CB	ALA- 184	3.99	0	Hydrophobic	false
N2	OG	SER- 185	2.74	174.82	H-Bond (Ligand Donor)	false
C2'	CZ	PHE- 190	4.13	0	Hydrophobic	false
N2	O	VAL- 200	2.77	127.54	H-Bond (Ligand Donor)	false
N1	O	VAL- 201	2.57	166.39	H-Bond (Ligand Donor)	false
N2	O	VAL- 201	3.4	126.28	H-Bond (Ligand Donor)	false
O2G	MG	MG- 1006	2.51	0	Metal Acceptor	false
O2B	MG	MG- 1006	2.14	0	Metal Acceptor	false
O1A	MG	MG- 1006	1.81	0	Metal Acceptor	false
O3'	O	HOH- 1009	2.87	165.67	H-Bond (Protein Donor)	false