scPDB - 1kyv entry

Protein Data Bank Entry:

PDB ID : 1kyv

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
B	35 %
C	65 %

Ligand binding site composition:

B-Factor:	35.792
Number of residues:	33
Including
Standard Amino Acids:	31
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.731	735.750

% Hydrophobic	% Polar
54.13	45.87
According to VolSite

Ligand :

HET Code:	RBF
Formula:	C17H20N4O6
Molecular weight:	376.364 g/mol
DrugBank ID:	DB00140
Buried Surface Area:	70.09 %
Polar Surface area:	155.04 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	5
Rings:	3
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
66.1279	18.0017	20.748

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
C1'	CE2	TRP- 27	3.71	0	Hydrophobic	false
C9A	CZ2	TRP- 27	3.45	0	Hydrophobic	false
O2	N	SER- 62	3	155.6	H-Bond (Protein Donor)	false
O2'	N	TRP- 63	3.02	165.93	H-Bond (Protein Donor)	false
C3'	CB	TRP- 63	3.62	0	Hydrophobic	false
O3'	OE1	GLU- 64	2.93	163.77	H-Bond (Ligand Donor)	false
O5'	OE2	GLU- 64	2.62	154.04	H-Bond (Ligand Donor)	false
N3	O	VAL- 86	2.84	174.29	H-Bond (Ligand Donor)	false
O4	N	ILE- 88	3.22	169.6	H-Bond (Protein Donor)	false
C7M	CB	HIS- 94	4.34	0	Hydrophobic	false
C6	CB	HIS- 94	4.37	0	Hydrophobic	false
DuAr	DuAr	HIS- 94	3.46	0	Aromatic Face/Face	false
C2'	CD1	ILE- 98	4.29	0	Hydrophobic	false
C5'	CG2	ILE- 118	3.67	0	Hydrophobic	false
O4'	O	LEU- 119	3.28	169.82	H-Bond (Ligand Donor)	false
C5'	CB	LEU- 119	3.55	0	Hydrophobic	false
C8M	CD2	LEU- 122	4.41	0	Hydrophobic	false
C7M	CD	ARG- 133	4.18	0	Hydrophobic	false
C8M	CZ2	TRP- 146	3.8	0	Hydrophobic	false
O2	O	HOH- 1005	3.05	179.96	H-Bond (Protein Donor)	false