scPDB - 1ejb entry

Protein Data Bank Entry:

PDB ID : 1ejb

Resolution :1.850 Å

Experimental Method : X-ray

Deposition Date : 2000-03-02

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:	RIB4_YEAST
AC:	P50861
Organism:	Saccharomyces cerevisiae
Reign:	Eukaryota
TaxID:	559292
EC Number:	2.5.1.78

Chains:

Chain Name:	Percentage of Residues within binding site
C	67 %
D	33 %

Ligand binding site composition:

B-Factor:	19.987
Number of residues:	38
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.816	810.000

% Hydrophobic	% Polar
55.83	44.17
According to VolSite

Ligand :

HET Code:	INJ
Formula:	C14H24N3O9P
Molecular weight:	409.329 g/mol
DrugBank ID:	DB04266
Buried Surface Area:	70.53 %
Polar Surface area:	232.19 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	7
Rings:	1
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	12

Mass center Coordinates

X	Y	Z
67.1905	32.4042	41.3084

Binding mode :

What is Poseview ?

2D View
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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
C8	CE2	TRP- 26	3.55	0	Hydrophobic	false
C13	CZ3	TRP- 26	3.52	0	Hydrophobic	false
O2	N	SER- 60	2.82	143.69	H-Bond (Protein Donor)	false
O9	N	TYR- 61	3.05	170.73	H-Bond (Protein Donor)	false
C10	CB	TYR- 61	3.81	0	Hydrophobic	false
O10	OE1	GLU- 62	2.55	172.66	H-Bond (Ligand Donor)	false
O12	OE2	GLU- 62	2.61	160.8	H-Bond (Ligand Donor)	false
N3	O	VAL- 89	2.92	177.27	H-Bond (Ligand Donor)	false
C14	CD2	LEU- 90	4.24	0	Hydrophobic	false
O4	N	ILE- 91	3.27	160.35	H-Bond (Protein Donor)	false
O3P	N	SER- 94	2.89	165.35	H-Bond (Protein Donor)	false
O2P	OG1	THR- 95	2.53	171.49	H-Bond (Protein Donor)	false
O2P	N	THR- 95	2.79	151.37	H-Bond (Protein Donor)	false
C14	CB	HIS- 97	4.45	0	Hydrophobic	false
C16	CB	HIS- 97	4.03	0	Hydrophobic	false
C15	CB	PHE- 98	4.43	0	Hydrophobic	false
C14	CD1	ILE- 101	4.19	0	Hydrophobic	false
C9	CD1	ILE- 101	3.93	0	Hydrophobic	false
C12	CG2	ILE- 121	3.48	0	Hydrophobic	false
O11	O	PHE- 122	3.02	166.49	H-Bond (Ligand Donor)	false
C12	CB	PHE- 122	4.16	0	Hydrophobic	false
O12	N	PHE- 122	2.8	150.49	H-Bond (Protein Donor)	false
O1P	CZ	ARG- 136	3.44	0	Ionic (Protein Cationic)	false
O3P	CZ	ARG- 136	3.69	0	Ionic (Protein Cationic)	false
O1P	NE	ARG- 136	2.66	174.72	H-Bond (Protein Donor)	false
O1P	NH2	ARG- 136	3.35	129.34	H-Bond (Protein Donor)	false
O3P	NH2	ARG- 136	2.73	168.21	H-Bond (Protein Donor)	false
O2	O	HOH- 409	3.03	179.94	H-Bond (Protein Donor)	false
O2P	O	HOH- 1310	2.74	179.96	H-Bond (Protein Donor)	false