scPDB - 1kyy entry

Protein Data Bank Entry:

PDB ID : 1kyy

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2002-02-06

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_SCHPO
AC:	Q9UUB1
Organism:	Schizosaccharomyces pombe
Reign:	Eukaryota
TaxID:	284812
EC Number:	2.5.1.78

Chains:

Chain Name:	Percentage of Residues within binding site
A	27 %
B	73 %

Ligand binding site composition:

B-Factor:	33.322
Number of residues:	33
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.438	752.625

% Hydrophobic	% Polar
44.84	55.16
According to VolSite

Ligand :

HET Code:	INI
Formula:	C9H14N4O8
Molecular weight:	306.229 g/mol
DrugBank ID:	DB04162
Buried Surface Area:	68.88 %
Polar Surface area:	196.96 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	7
Rings:	1
Aromatic rings:	0
Anionic atoms:	1
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
75.3599	23.3369	39.0099

Binding mode :

What is Poseview ?

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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
O2	N	SER- 62	2.88	145.63	H-Bond (Protein Donor)	false
O9	N	TRP- 63	3.01	171.43	H-Bond (Protein Donor)	false
C9	CB	TRP- 63	3.52	0	Hydrophobic	false
O10	OE1	GLU- 64	3.11	142.98	H-Bond (Ligand Donor)	false
O12	OE2	GLU- 64	2.51	161.4	H-Bond (Ligand Donor)	false
N3	O	VAL- 86	2.79	172.81	H-Bond (Ligand Donor)	false
O4	N	ILE- 88	3.42	161.17	H-Bond (Protein Donor)	false
C8	CD1	ILE- 98	3.61	0	Hydrophobic	false
C12	CB	ILE- 118	4.28	0	Hydrophobic	false
O11	O	LEU- 119	3.26	178.5	H-Bond (Ligand Donor)	false
C12	CB	LEU- 119	4.04	0	Hydrophobic	false
O12	N	LEU- 119	2.85	152.85	H-Bond (Protein Donor)	false
O2	O	HOH- 1003	2.82	179.96	H-Bond (Protein Donor)	false