scPDB - 3ix9 entry

Protein Data Bank Entry:

PDB ID : 3ix9

Resolution :1.950 Å

Experimental Method : X-ray

Deposition Date : 2009-09-03

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Dihydrofolate reductase
ID:	DYR_STRPN
AC:	Q54801
Organism:	Streptococcus pneumoniae serotype 4
Reign:	Bacteria
TaxID:	170187
EC Number:	1.5.1.3

Chains:

Chain Name:	Percentage of Residues within binding site
A	8 %
B	92 %

Ligand binding site composition:

B-Factor:	27.492
Number of residues:	41
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:	NDP
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.858	914.625

% Hydrophobic	% Polar
51.29	48.71
According to VolSite

Ligand :

HET Code:	MTX
Formula:	C20H20N8O5
Molecular weight:	452.423 g/mol
DrugBank ID:	DB00563
Buried Surface Area:	66.45 %
Polar Surface area:	216.2 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	3
Rings:	3
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
-18.8185	-14.2323	-21.2683

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
NA4	O	ILE- 8	2.8	162.82	H-Bond (Ligand Donor)	false
CM	CD1	LEU- 23	3.71	0	Hydrophobic	false
N1	OE1	GLU- 30	2.78	174.79	H-Bond (Ligand Donor)	false
NA2	OE2	GLU- 30	2.75	178.61	H-Bond (Ligand Donor)	false
C15	CD2	LEU- 31	4.18	0	Hydrophobic	false
CG	CB	LEU- 31	3.45	0	Hydrophobic	false
C11	CD2	LEU- 31	3.97	0	Hydrophobic	false
CB	CB	LYS- 35	3.85	0	Hydrophobic	false
CM	CB	MET- 53	4.23	0	Hydrophobic	false
C14	SD	MET- 53	4.18	0	Hydrophobic	false
C15	CE	MET- 53	4.48	0	Hydrophobic	false
C13	CE	MET- 53	4.09	0	Hydrophobic	false
O	NH1	ARG- 56	2.94	148.16	H-Bond (Protein Donor)	false
C11	CD2	LEU- 58	4.16	0	Hydrophobic	false
C16	CD1	LEU- 58	4.2	0	Hydrophobic	false
O1	NH1	ARG- 61	2.84	167.39	H-Bond (Protein Donor)	false
O1	NH2	ARG- 61	3.38	134.41	H-Bond (Protein Donor)	false
O2	NH2	ARG- 61	2.71	166.94	H-Bond (Protein Donor)	false
O1	CZ	ARG- 61	3.56	0	Ionic (Protein Cationic)	false
O2	CZ	ARG- 61	3.66	0	Ionic (Protein Cationic)	false
NA4	O	VAL- 100	2.57	124.63	H-Bond (Ligand Donor)	false
N8	O	HOH- 188	3.07	179.98	H-Bond (Protein Donor)	false
NA2	O	HOH- 244	2.87	131.49	H-Bond (Ligand Donor)	false