scPDB - 2dhf entry

Protein Data Bank Entry:

PDB ID : 2dhf

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 1989-10-25

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
B	100 %

Ligand binding site composition:

B-Factor:	34.945
Number of residues:	35
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.286	1140.750

% Hydrophobic	% Polar
49.70	50.30
According to VolSite

Ligand :

HET Code:	DZF
Formula:	C20H18N6O6
Molecular weight:	438.394 g/mol
DrugBank ID:	-
Buried Surface Area:	61.9 %
Polar Surface area:	201.76 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
10.956	26.4235	68.7897

Binding mode :

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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
N8	O	ILE- 7	2.75	172.98	H-Bond (Ligand Donor)	false
C5	CD2	LEU- 22	4.41	0	Hydrophobic	false
NA2	OE2	GLU- 30	3.46	131.23	H-Bond (Ligand Donor)	false
N3	OE2	GLU- 30	2.7	163.09	H-Bond (Ligand Donor)	false
CG	CB	PHE- 31	3.43	0	Hydrophobic	false
CG	CB	GLN- 35	4.35	0	Hydrophobic	false
O1	NE2	GLN- 35	2.74	148.36	H-Bond (Protein Donor)	false
C9	CG2	THR- 56	3.76	0	Hydrophobic	false
C16	CG1	ILE- 60	3.78	0	Hydrophobic	false
O	ND2	ASN- 64	2.67	129.5	H-Bond (Protein Donor)	false
O1	CZ	ARG- 70	3.79	0	Ionic (Protein Cationic)	false
O2	CZ	ARG- 70	3.42	0	Ionic (Protein Cationic)	false
O1	NH2	ARG- 70	2.78	161.25	H-Bond (Protein Donor)	false
O2	NH1	ARG- 70	2.77	153.6	H-Bond (Protein Donor)	false
O2	NH2	ARG- 70	3.18	135.13	H-Bond (Protein Donor)	false
NA2	O	HOH- 402	3.36	150.43	H-Bond (Ligand Donor)	false