scPDB - 3irm entry

Protein Data Bank Entry:

PDB ID : 3irm

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2009-08-24

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Bifunctional dihydrofolate reductase-thymidylate synthase
ID:	DRTS_TRYCR
AC:	Q27793
Organism:	Trypanosoma cruzi
Reign:	Eukaryota
TaxID:	5693
EC Number:	1.5.1.3

Chains:

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

Ligand binding site composition:

B-Factor:	31.896
Number of residues:	26
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.458	968.625

% Hydrophobic	% Polar
58.89	41.11
According to VolSite

Ligand :

HET Code:	1CY
Formula:	C11H16ClN5
Molecular weight:	253.731 g/mol
DrugBank ID:	-
Buried Surface Area:	62.47 %
Polar Surface area:	83.22 Å2

Number of
H-Bond Acceptors:	0
H-Bond Donors:	4
Rings:	2
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	2
Rule of Five Violation:	0
Rotatable Bonds:	1

Mass center Coordinates

X	Y	Z
11.3439	-25.5277	-16.5361

Binding mode :

What is Poseview ?

2D View
3D View

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
N8	O	VAL- 26	3.06	165.93	H-Bond (Ligand Donor)	false
C10	CB	ALA- 28	3.91	0	Hydrophobic	false
C16	CD1	ILE- 41	3.72	0	Hydrophobic	false
N1	OD2	ASP- 48	2.58	143.15	H-Bond (Protein Donor)	false
N7	OD1	ASP- 48	3.19	159.86	H-Bond (Ligand Donor)	false
C9	SD	MET- 49	4.25	0	Hydrophobic	false
C9	CB	PHE- 52	3.55	0	Hydrophobic	false
C12	CE2	PHE- 52	3.46	0	Hydrophobic	false
CL17	CG2	THR- 80	3.48	0	Hydrophobic	false
CL17	CG1	ILE- 84	3.48	0	Hydrophobic	false
N8	O	ILE- 154	2.85	127.64	H-Bond (Ligand Donor)	false
CL17	CD1	ILE- 154	4.24	0	Hydrophobic	false
C13	CD1	ILE- 154	4.05	0	Hydrophobic	false