scPDB - 4ddr entry

Protein Data Bank Entry:

PDB ID : 4ddr

Resolution :2.050 Å

Experimental Method : X-ray

Deposition Date : 2012-01-19

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_HUMAN
AC:	P00374
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	1.5.1.3

Chains:

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

Ligand binding site composition:

B-Factor:	26.156
Number of residues:	35
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:	NDP
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.111	519.750

% Hydrophobic	% Polar
64.94	35.06
According to VolSite

Ligand :

HET Code:	MMV
Formula:	C18H23N4O4
Molecular weight:	359.400 g/mol
DrugBank ID:	-
Buried Surface Area:	70.64 %
Polar Surface area:	136.41 Å2

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

Mass center Coordinates

X	Y	Z
30.6884	13.6355	-1.11554

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
N7	O	ILE- 7	2.93	156	H-Bond (Ligand Donor)	false
C9	CD1	LEU- 22	4.13	0	Hydrophobic	false
C19	CG	LEU- 22	3.76	0	Hydrophobic	false
C21	CD2	LEU- 22	3.6	0	Hydrophobic	false
N4	OE2	GLU- 30	3.49	128.82	H-Bond (Ligand Donor)	false
N4	OE1	GLU- 30	2.62	178.06	H-Bond (Ligand Donor)	false
N8	OE2	GLU- 30	2.74	168.44	H-Bond (Ligand Donor)	false
C10	CD1	PHE- 31	3.54	0	Hydrophobic	false
C23	CE1	PHE- 31	3.66	0	Hydrophobic	false
C10	CB	PHE- 34	4.22	0	Hydrophobic	false
C12	CZ	PHE- 34	3.66	0	Hydrophobic	false
C13	CG2	THR- 56	4.08	0	Hydrophobic	false
C21	CB	SER- 59	3.91	0	Hydrophobic	false
C16	CG1	ILE- 60	4.44	0	Hydrophobic	false
C14	CG1	ILE- 60	4.01	0	Hydrophobic	false
C18	CG	PRO- 61	4.41	0	Hydrophobic	false
C23	CG	PRO- 61	4.21	0	Hydrophobic	false
N7	O	VAL- 115	3.34	133.47	H-Bond (Ligand Donor)	false
C12	C4N	NDP- 201	4.46	0	Hydrophobic	false
C14	C5N	NDP- 201	4.04	0	Hydrophobic	false
C21	C2D	NDP- 201	4.15	0	Hydrophobic	false
N8	O	HOH- 1006	3.13	140.35	H-Bond (Ligand Donor)	false
O26	O	HOH- 1054	2.86	179.97	H-Bond (Protein Donor)	false