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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Protein Data Bank Entry:

3hy4

2.790 Å

X-ray

2009-06-22

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:5-formyltetrahydrofolate cyclo-ligase
ID:MTHFS_HUMAN
AC:P49914
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:6.3.3.2


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:31.525
Number of residues:28
Including
Standard Amino Acids: 28
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.398702.000

% Hydrophobic% Polar
50.9649.04
According to VolSite

Ligand :
3hy4_1 Structure
HET Code: N5G
Formula: C20H36N7O10P
Molecular weight: 565.514 g/mol
DrugBank ID: -
Buried Surface Area:40.7 %
Polar Surface area: 298.36 Å2
Number of
H-Bond Acceptors: 14
H-Bond Donors: 7
Rings: 3
Aromatic rings: 0
Anionic atoms: 4
Cationic atoms: 2
Rule of Five Violation: 3
Rotatable Bonds: 12

Mass center Coordinates

XYZ
-6.3076814.249810.9075


Binding mode :
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Binding mode
BioSolveIT 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
BioSolveIT


LigandProteinInteraction
AtomAtomResidueDistance
(Å)
Angle (°)Type
N3OE2GLU- 613.350Ionic
(Ligand Cationic)
C13CE2TYR- 833.440Hydrophobic
C13CE2TRP- 1094.150Hydrophobic
C11CE2TRP- 1093.750Hydrophobic
C15CZ2TRP- 1093.250Hydrophobic
O4NEARG- 1483.26129.78H-Bond
(Protein Donor)
CGCDLYS- 1503.910Hydrophobic
C16CDLYS- 1503.620Hydrophobic
C13CE1TYR- 1524.060Hydrophobic