scPDB - 1k0c entry

Protein Data Bank Entry:

PDB ID : 1k0c

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2001-09-19

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Transcriptional regulator URE2
ID:	URE2_YEAST
AC:	P23202
Organism:	Saccharomyces cerevisiae
Reign:	Eukaryota
TaxID:	559292
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
C	85 %
D	15 %

Ligand binding site composition:

B-Factor:	27.459
Number of residues:	37
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.540	867.375

% Hydrophobic	% Polar
37.74	62.26
According to VolSite

Ligand :

HET Code:	GTB
Formula:	C17H21N4O8S
Molecular weight:	441.436 g/mol
DrugBank ID:	DB03686
Buried Surface Area:	53.51 %
Polar Surface area:	237.22 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	3
Rings:	1
Aromatic rings:	1
Anionic atoms:	3
Cationic atoms:	2
Rule of Five Violation:	1
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
30.782	-2.03177	14.1397

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
SG2	CB	ALA- 122	4.11	0	Hydrophobic	false
C3'	CG	PRO- 123	4.07	0	Hydrophobic	false
SG2	CB	ASN- 124	4.25	0	Hydrophobic	false
CB2	CZ	PHE- 146	4.44	0	Hydrophobic	false
CG1	CB	ARG- 164	4.27	0	Hydrophobic	false
O32	CZ	ARG- 164	2.96	0	Ionic (Protein Cationic)	false
N2	O	VAL- 165	2.87	149.64	H-Bond (Ligand Donor)	false
O2	N	VAL- 165	2.99	167.31	H-Bond (Protein Donor)	false
CB2	CG2	VAL- 165	4.35	0	Hydrophobic	false
N1	OE2	GLU- 180	2.84	161.28	H-Bond (Ligand Donor)	false
N1	OE2	GLU- 180	2.84	0	Ionic (Ligand Cationic)	false
N1	OE1	GLU- 180	3.3	0	Ionic (Ligand Cationic)	false
O11	N	SER- 181	3.48	143.39	H-Bond (Protein Donor)	false
O11	OG	SER- 181	2.62	157.68	H-Bond (Protein Donor)	false
O12	N	SER- 181	2.93	162.09	H-Bond (Protein Donor)	false
C3'	CD1	LEU- 231	3.57	0	Hydrophobic	false
C2'	CZ3	TRP- 316	3.49	0	Hydrophobic	false
SG2	CH2	TRP- 316	4.45	0	Hydrophobic	false
O42	CZ	ARG- 322	3.47	0	Ionic (Protein Cationic)	false
O12	O	HOH- 366	2.6	164.99	H-Bond (Protein Donor)	false
O11	O	HOH- 377	2.84	150.62	H-Bond (Protein Donor)	false