scPDB - 1rp0 entry

Protein Data Bank Entry:

PDB ID : 1rp0

Resolution :1.600 Å

Experimental Method : X-ray

Deposition Date : 2003-12-02

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Thiamine thiazole synthase, chloroplastic
ID:	THI4_ARATH
AC:	Q38814
Organism:	Arabidopsis thaliana
Reign:	Eukaryota
TaxID:	3702
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	14.371
Number of residues:	52
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	1
Water Molecules:	5
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.446	627.750

% Hydrophobic	% Polar
33.33	66.67
According to VolSite

Ligand :

HET Code:	AHZ
Formula:	C17H19N6O12P2S
Molecular weight:	593.378 g/mol
DrugBank ID:	DB04362
Buried Surface Area:	72.32 %
Polar Surface area:	328.14 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	3
Rings:	4
Aromatic rings:	3
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
54.6608	21.1608	34.8078

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
O1B	N	ALA- 50	2.9	161.41	H-Bond (Protein Donor)	false
O2'	OE2	GLU- 70	2.71	171.81	H-Bond (Ligand Donor)	false
O3'	OE1	GLU- 70	2.69	173.14	H-Bond (Ligand Donor)	false
O2'	NE2	GLN- 71	2.93	157.41	H-Bond (Protein Donor)	false
N3	N	GLN- 71	3.05	142.44	H-Bond (Protein Donor)	false
C1'	CG	GLN- 71	4.44	0	Hydrophobic	false
O2A	N	GLY- 78	2.85	169.65	H-Bond (Protein Donor)	false
N1	N	ALA- 143	3.01	162.08	H-Bond (Protein Donor)	false
N6	O	ALA- 143	2.77	163.69	H-Bond (Ligand Donor)	false
N6	OG1	THR- 196	3.11	170.21	H-Bond (Ligand Donor)	false
O2B	N	MET- 241	2.86	161.48	H-Bond (Protein Donor)	false
S1T	CG	MET- 241	3.55	0	Hydrophobic	false
C7T	CG	MET- 241	3.59	0	Hydrophobic	false
O1R	NH2	ARG- 251	2.71	157.67	H-Bond (Protein Donor)	false
O2R	NE	ARG- 251	3.15	172.76	H-Bond (Protein Donor)	false
O1R	CZ	ARG- 251	3.58	0	Ionic (Protein Cationic)	false
O2R	CZ	ARG- 251	3.89	0	Ionic (Protein Cationic)	false
S1T	SD	MET- 252	3.81	0	Hydrophobic	false
O2R	N	GLY- 253	3.16	138.52	H-Bond (Protein Donor)	false
C7T	SD	MET- 259	3.46	0	Hydrophobic	false
C6T	CG	MET- 259	4	0	Hydrophobic	false
O1R	ZN	ZN- 500	2.07	0	Metal Acceptor	false
N3T	ZN	ZN- 500	2.1	0	Metal Acceptor	false
DuAr	ZN	ZN- 500	3.26	86.64	Pi/Cation	false
O3'	O	HOH- 745	2.9	123.59	H-Bond (Protein Donor)	false
O1B	O	HOH- 798	2.72	161.24	H-Bond (Protein Donor)	false
O2B	O	HOH- 799	2.66	149.99	H-Bond (Protein Donor)	false
O1A	O	HOH- 802	2.57	149.99	H-Bond (Protein Donor)	false