scPDB - 2c97 entry

Protein Data Bank Entry:

PDB ID : 2c97

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2005-12-09

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	6,7-dimethyl-8-ribityllumazine synthase
ID:	RISB_MYCTU
AC:	P9WHE9
Organism:	Mycobacterium tuberculosis
Reign:	Bacteria
TaxID:	83332
EC Number:	2.5.1.78

Chains:

Chain Name:	Percentage of Residues within binding site
C	78 %
D	22 %

Ligand binding site composition:

B-Factor:	27.682
Number of residues:	29
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.356	546.750

% Hydrophobic	% Polar
50.00	50.00
According to VolSite

Ligand :

HET Code:	JCL
Formula:	C8H10ClN2O6P
Molecular weight:	296.602 g/mol
DrugBank ID:	DB08016
Buried Surface Area:	64.17 %
Polar Surface area:	140.43 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	2
Rings:	1
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
6.02106	10.294	21.2007

Binding mode :

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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
C7	CZ2	TRP- 27	4.29	0	Hydrophobic	false
O1	N	ALA- 59	2.66	164.65	H-Bond (Protein Donor)	false
N1	O	VAL- 81	2.92	166.27	H-Bond (Ligand Donor)	false
CL	CG1	VAL- 82	3.92	0	Hydrophobic	false
C8	CG1	VAL- 82	4.37	0	Hydrophobic	false
CL	CB	ILE- 83	4.3	0	Hydrophobic	false
O3P	N	GLN- 86	2.74	153.42	H-Bond (Protein Donor)	false
O2P	OG1	THR- 87	2.59	169.23	H-Bond (Protein Donor)	false
O2P	N	THR- 87	3.05	149.15	H-Bond (Protein Donor)	false
C9	CB	HIS- 89	4.3	0	Hydrophobic	false
O1P	NE	ARG- 128	2.66	170.71	H-Bond (Protein Donor)	false
O1P	NH2	ARG- 128	3.27	130.38	H-Bond (Protein Donor)	false
O3P	NH2	ARG- 128	3.06	165.82	H-Bond (Protein Donor)	false
O1P	CZ	ARG- 128	3.39	0	Ionic (Protein Cationic)	false
O1	O	HOH- 2005	2.91	160.04	H-Bond (Protein Donor)	false