Quick start — draw your first molecule
Click the carbon button (or press C) in Ketcher's left toolbar.
Click in the canvas — methane (CH₄) appears (hydrogens are hidden but present).
Click one of the hydrogen positions to add another carbon. Repeat to build a chain.
Want a benzene ring ? Click the hexagon icon (or press 5) and place it.
Click 🔍 Search local in the right side-panel when done.
The SMILES string updates live below the canvas while you work.
Toolbar — what the buttons do
Ketcher's toolbar runs along the left side. Grouped top-down:
Select / move — arrow (or Esc). Click-and-drag to select; move atoms/groups.Erase — broom (or Del). Click atom/bond to remove.Bond types — single, double, triple, aromatic, stereo (wedge up/down). Click the type first, then a bond to change it. Shortcuts: 1, 2, 3.Atoms — carbon is default. Click another element button (H, O, N, S, P, F, Cl, Br, I) or open the periodic table for more. Shortcuts: C, O, N, S, H.Rings (template) — benzene (6-ring w/ double bonds), cyclohexane, cyclopentane and more. Click a ring first, then in the canvas or on an existing atom to fuse.Functional templates — e.g. carboxylic acid, ester, sulfonamide. Shortcuts for common groups.Charge / radicals — +, −, dots for radicals.R-groups / abbreviations — for drawing generic substituents (R₁, R₂…).
Atoms — adding specific elements
Common atoms are toolbar buttons — click e.g. O, then in the canvas.Uncommon atoms : click "Periodic table" or press A for the atom dialog — pick any element.Change atom at a position : double-click the atom → change symbol → OK.Implicit hydrogens are hidden but present. To show: View → Show hydrogens in Ketcher's menu.Isotopes : double-click atom → set mass in the "Isotope" field (e.g. 13 for ¹³C).
Bonds — types and stereochemistry
Click a bond while a bond type is selected → changes its type.Cycle types : click the same bond repeatedly (single → double → triple → single).Stereochemistry — wedge bonds (▲/▽) indicate a group pointing up/down from the plane (3D info in a 2D drawing). Important for chiral centres.Cis/trans (E/Z) — drawn naturally by how the double-bond substituents are placed.Aromatic rings : use either the benzene template, or draw alternating single/double bonds. Ketcher interprets both correctly.
Rings and templates
Benzene (6-ring w/ double bonds): click the benzene icon, then in the canvas.Fuse rings : with benzene selected, click an existing bond or atom → the ring is fused on.Custom ring size : hover over the ring icon for a menu of 3–8-rings, or use "Custom Ring" .Hetero rings (pyridine, furan, thiophene): after placing a carbon ring, change the right atoms via double-click.
Select, copy, move
Select fragment : arrow tool + drag box around atoms.Select all : Ctrl/⌘ + A.Copy / cut / paste : standard Ctrl/⌘ + C/X/V.Rotate selection : Ctrl/⌘ + drag inside the selection.Undo/redo : Ctrl/⌘ + Z / Ctrl/⌘ + Y.
Import and export
Paste SMILES or MOL : File → Paste from clipboard . Ketcher auto-detects format.Open file : File → Open — supports MOL, RXN, SMILES, InChI, CML and more.Save : File → Save As — pick format. SMILES is smallest and most portable.Auto-save : the drawing is stored in the browser and restored on next visit (and across language switches).
Tips and common problems
"Nothing happens when I click" — check that the right tool is active in the left panel (selected button glows blue).Wrong bond type — click the bond type in the toolbar first, then the bond.Two atoms aren't connected — select both → choose bond type → click between them."Clear canvas" button in the right panel resets everything.More Ketcher help : EPAM Ketcher official docs .
After drawing — how the app looks up the substance
When you click Search local , an InChIKey (structural hash) is computed
and matched against the database:
Exact hit — full InChIKey matches incl. stereochemistry/isotopes/charge. "Same" substance.Skeleton hit — only the first 14 characters match (same connectivity, possible stereo difference).No hit — optional PubChem online search.
The result card then shows the SvSID, CAS, name, hazard classification (Annex VI + ECHA C&L),
physical properties and a
Hover over badges and tags to see what they mean.