scPDB - 2jlb entry

Protein Data Bank Entry:

PDB ID : 2jlb

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2008-09-07

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Uncharacterized protein
ID:	Q8PC69_XANCP
AC:	Q8PC69
Organism:	Xanthomonas campestris pv. campestris
Reign:	Bacteria
TaxID:	190485
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	24.736
Number of residues:	48
Including
Standard Amino Acids:	47
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.605	479.250

% Hydrophobic	% Polar
47.89	52.11
According to VolSite

Ligand :

HET Code:	UDM
Formula:	C18H27N3O16P2
Molecular weight:	603.365 g/mol
DrugBank ID:	-
Buried Surface Area:	59.77 %
Polar Surface area:	316.45 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	7
Rings:	3
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
20.3502	11.8132	26.3293

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
C5'	CG	PRO- 219	4.41	0	Hydrophobic	false
CB	CG	PRO- 219	3.76	0	Hydrophobic	false
C3'	CB	PRO- 219	3.56	0	Hydrophobic	false
C4D	CG	PRO- 219	4.16	0	Hydrophobic	false
O3'	OG1	THR- 220	3.2	153.72	H-Bond (Ligand Donor)	false
C8'	CD1	LEU- 223	4.08	0	Hydrophobic	false
C8'	CG	LEU- 313	4.01	0	Hydrophobic	false
O1A	ND2	ASN- 385	3.24	137.07	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 388	3.91	0	Ionic (Protein Cationic)	false
O2B	NZ	LYS- 388	2.96	0	Ionic (Protein Cationic)	false
O2B	NZ	LYS- 388	2.96	154.23	H-Bond (Protein Donor)	false
N3	O	LEU- 442	2.82	160.11	H-Bond (Ligand Donor)	false
O4	N	LEU- 442	3.13	150.3	H-Bond (Protein Donor)	false
C2D	CE2	TYR- 447	3.77	0	Hydrophobic	false
C3D	CG2	THR- 467	3.98	0	Hydrophobic	false
O1B	OG1	THR- 467	2.74	158.5	H-Bond (Protein Donor)	false
O1B	N	THR- 467	3.01	164.03	H-Bond (Protein Donor)	false
C2D	CG2	THR- 468	4.26	0	Hydrophobic	false
O2'	OD2	ASP- 471	2.59	154.45	H-Bond (Ligand Donor)	false
O3A	O	HOH- 2059	2.87	179.98	H-Bond (Protein Donor)	false