scPDB - 1kyx entry

Protein Data Bank Entry:

PDB ID : 1kyx

Resolution :2.600 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
C	28 %
D	72 %

Ligand binding site composition:

B-Factor:	38.800
Number of residues:	38
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.666	749.250

% Hydrophobic	% Polar
44.14	55.86
According to VolSite

Ligand :

HET Code:	CRM
Formula:	C14H17N4O9
Molecular weight:	385.306 g/mol
DrugBank ID:	DB03883
Buried Surface Area:	66.89 %
Polar Surface area:	211.91 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	6
Rings:	2
Aromatic rings:	0
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
60.4301	37.0449	9.05789

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
C17	CE2	TRP- 27	3.82	0	Hydrophobic	false
C11	CH2	TRP- 27	3.86	0	Hydrophobic	false
O14	ND2	ASN- 28	3.46	147.62	H-Bond (Protein Donor)	false
O15	N	SER- 62	2.95	149.2	H-Bond (Protein Donor)	false
O15	OG	SER- 62	2.61	156.55	H-Bond (Protein Donor)	false
O19	N	TRP- 63	2.93	161.93	H-Bond (Protein Donor)	false
C20	CB	TRP- 63	3.58	0	Hydrophobic	false
O26	OE2	GLU- 64	2.64	152.94	H-Bond (Ligand Donor)	false
O21	OE2	GLU- 64	3.3	141.77	H-Bond (Ligand Donor)	false
O21	OE1	GLU- 64	2.65	158.39	H-Bond (Ligand Donor)	false
N1	O	VAL- 86	2.54	175.63	H-Bond (Ligand Donor)	false
O14	N	ILE- 88	3.3	168.86	H-Bond (Protein Donor)	false
C12	CB	HIS- 94	4.09	0	Hydrophobic	false
C18	CD1	ILE- 98	4.22	0	Hydrophobic	false
C25	CG2	ILE- 118	3.72	0	Hydrophobic	false
C25	CB	LEU- 119	4.4	0	Hydrophobic	false
O26	N	LEU- 119	2.91	140.39	H-Bond (Protein Donor)	false
O23	O	LEU- 119	3.07	165.53	H-Bond (Ligand Donor)	false
O15	O	HOH- 1007	2.73	147.76	H-Bond (Protein Donor)	false