diff --git a/packages/core/src/components/scatter-plot/context-menu.styles.ts b/packages/core/src/components/scatter-plot/context-menu.styles.ts
new file mode 100644
index 00000000..f39f7f56
--- /dev/null
+++ b/packages/core/src/components/scatter-plot/context-menu.styles.ts
@@ -0,0 +1,66 @@
+// packages/core/src/components/scatter-plot/context-menu.styles.ts
+import { css } from 'lit';
+
+export const contextMenuStyles = css`
+  :host {
+    position: absolute;
+    z-index: var(--z-dropdown, 100);
+    pointer-events: auto;
+  }
+
+  .menu {
+    position: absolute;
+    background: var(--surface, #fff);
+    border: var(--border-width, 1px) solid var(--border, #e2e8f0);
+    border-radius: var(--radius, 6px);
+    padding: 4px 0;
+    min-width: 180px;
+    box-shadow: var(--shadow-lg, 0 8px 30px rgba(0, 0, 0, 0.12));
+    font-size: var(--text-base, 12px);
+    font-family: inherit;
+  }
+
+  .menu-item {
+    display: flex;
+    align-items: center;
+    gap: 10px;
+    padding: 7px 14px;
+    color: var(--text-primary, #334155);
+    cursor: pointer;
+    border: none;
+    background: none;
+    width: 100%;
+    text-align: left;
+    font: inherit;
+  }
+
+  .menu-item:hover {
+    background: var(--primary-light, #eef6fb);
+    color: var(--primary, #00a3e0);
+  }
+
+  .menu-item[aria-disabled='true'] {
+    color: var(--text-tertiary, #a0aec0);
+    cursor: default;
+    pointer-events: none;
+  }
+
+  .menu-item .icon {
+    width: 16px;
+    text-align: center;
+    font-size: 13px;
+    flex-shrink: 0;
+  }
+
+  .menu-item .shortcut {
+    margin-left: auto;
+    font-size: var(--text-xs, 10px);
+    color: var(--text-secondary, #5b6b7a);
+  }
+
+  .separator {
+    height: 1px;
+    background: var(--border, #e2e8f0);
+    margin: 4px 0;
+  }
+`;
diff --git a/packages/core/src/components/scatter-plot/context-menu.test.ts b/packages/core/src/components/scatter-plot/context-menu.test.ts
new file mode 100644
index 00000000..c51dc84e
--- /dev/null
+++ b/packages/core/src/components/scatter-plot/context-menu.test.ts
@@ -0,0 +1,32 @@
+// packages/core/src/components/scatter-plot/context-menu.test.ts
+import { describe, it, expect } from 'vitest';
+import { resolveMenuItems } from './context-menu';
+
+describe('context-menu', () => {
+  describe('resolveMenuItems', () => {
+    it('returns point actions when a point is hit', () => {
+      const items = resolveMenuItems({
+        proteinId: 'P0DM09',
+        hasAccession: true,
+        dataCoords: [10, 20],
+      });
+      const types = items.map((i) => i.action.type);
+      expect(types).toContain('copy-id');
+      expect(types).toContain('view-uniprot');
+    });
+
+    it('disables view-uniprot when no accession', () => {
+      const items = resolveMenuItems({
+        proteinId: 'custom_001',
+        hasAccession: false,
+        dataCoords: [10, 20],
+      });
+      const uniprotItem = items.find((i) => i.action.type === 'view-uniprot');
+      expect(uniprotItem?.disabled).toBe(true);
+    });
+
+    it('returns no items when no point is hit', () => {
+      expect(resolveMenuItems(null)).toEqual([]);
+    });
+  });
+});
diff --git a/packages/core/src/components/scatter-plot/context-menu.ts b/packages/core/src/components/scatter-plot/context-menu.ts
new file mode 100644
index 00000000..20e19f29
--- /dev/null
+++ b/packages/core/src/components/scatter-plot/context-menu.ts
@@ -0,0 +1,124 @@
+// packages/core/src/components/scatter-plot/context-menu.ts
+import { LitElement, html, nothing } from 'lit';
+import { customElement, property } from 'lit/decorators.js';
+import { contextMenuStyles } from './context-menu.styles';
+
+export interface ContextMenuAction {
+  type: 'copy-id' | 'view-uniprot';
+  proteinId: string;
+}
+
+export interface MenuItem {
+  label: string;
+  icon: string;
+  action: ContextMenuAction;
+  shortcut?: string;
+  disabled?: boolean;
+  separator?: boolean;
+}
+
+interface PointHit {
+  proteinId: string;
+  hasAccession: boolean;
+  dataCoords: [number, number];
+}
+
+export function resolveMenuItems(hit: PointHit | null): MenuItem[] {
+  if (!hit) return [];
+  return [
+    {
+      label: 'Copy ID',
+      icon: '📋',
+      action: { type: 'copy-id', proteinId: hit.proteinId },
+    },
+    {
+      label: 'View in UniProt',
+      icon: '🔗',
+      action: { type: 'view-uniprot', proteinId: hit.proteinId },
+      disabled: !hit.hasAccession,
+    },
+  ];
+}
+
+@customElement('protspace-context-menu')
+class ProtspaceContextMenu extends LitElement {
+  static styles = contextMenuStyles;
+
+  @property({ type: Boolean }) open = false;
+  @property({ type: Array }) items: MenuItem[] = [];
+
+  // Use composedPath() to correctly detect clicks inside nested shadow DOMs.
+  // With nested shadow DOM, e.target at the document level is retargeted to
+  // the outermost shadow host, so this.contains(e.target) always returns false.
+  private _onClickOutside = (e: MouseEvent) => {
+    if (!e.composedPath().includes(this)) {
+      this._close();
+    }
+  };
+
+  private _onEscape = (e: KeyboardEvent) => {
+    if (e.key === 'Escape') {
+      this._close();
+    }
+  };
+
+  connectedCallback() {
+    super.connectedCallback();
+    document.addEventListener('mousedown', this._onClickOutside);
+    document.addEventListener('keydown', this._onEscape);
+  }
+
+  disconnectedCallback() {
+    document.removeEventListener('mousedown', this._onClickOutside);
+    document.removeEventListener('keydown', this._onEscape);
+    super.disconnectedCallback();
+  }
+
+  private _close() {
+    this.open = false;
+    this.dispatchEvent(new CustomEvent('context-menu-close'));
+  }
+
+  private _handleItemClick(item: MenuItem) {
+    if (item.disabled) return;
+    this.dispatchEvent(
+      new CustomEvent<ContextMenuAction>('context-menu-action', {
+        detail: item.action,
+        bubbles: true,
+        composed: true,
+      }),
+    );
+    this._close();
+  }
+
+  render() {
+    if (!this.open) return nothing;
+
+    return html`
+      <div class="menu" role="menu">
+        ${this.items.map((item) =>
+          item.separator
+            ? html`<div class="separator"></div>`
+            : html`
+                <button
+                  class="menu-item"
+                  role="menuitem"
+                  aria-disabled="${item.disabled ? 'true' : 'false'}"
+                  @click="${() => this._handleItemClick(item)}"
+                >
+                  <span class="icon">${item.icon}</span>
+                  <span>${item.label}</span>
+                  ${item.shortcut ? html`<span class="shortcut">${item.shortcut}</span>` : nothing}
+                </button>
+              `,
+        )}
+      </div>
+    `;
+  }
+}
+
+declare global {
+  interface HTMLElementTagNameMap {
+    'protspace-context-menu': ProtspaceContextMenu;
+  }
+}
diff --git a/packages/core/src/components/scatter-plot/scatter-plot.ts b/packages/core/src/components/scatter-plot/scatter-plot.ts
index aedcb63a..c7f1da08 100644
--- a/packages/core/src/components/scatter-plot/scatter-plot.ts
+++ b/packages/core/src/components/scatter-plot/scatter-plot.ts
@@ -18,6 +18,8 @@ import { scatterplotStyles } from './scatter-plot.styles';
 import './projection-metadata';
 import './protspace-tips';
 import './protein-tooltip';
+import './context-menu';
+import { resolveMenuItems, type MenuItem, type ContextMenuAction } from './context-menu';
 import { DEFAULT_CONFIG } from './config';
 import { createStyleGetters } from './style-getters';
 import { MAX_POINTS_DIRECT_RENDER, WebGLRenderer } from './webgl';
@@ -76,6 +78,10 @@ export class ProtspaceScatterplot extends LitElement {
   @property({ type: Boolean, attribute: 'show-tour-button' }) showTourButton = false;
 
   // State
+  @state() private _contextMenuOpen = false;
+  @state() private _contextMenuX = 0;
+  @state() private _contextMenuY = 0;
+  @state() private _contextMenuItems: MenuItem[] = [];
   @state() private _plotData: PlotDataPoint[] = [];
   @state() private _tooltipData: {
     x: number;
@@ -2037,12 +2043,66 @@ export class ProtspaceScatterplot extends LitElement {
     return `left: ${left}px; top: ${top}px;${transform ? ` transform: ${transform};` : ''}`;
   }
 
+  private _hitTestAtClient(
+    clientX: number,
+    clientY: number,
+  ): { proteinId: string; dataCoords: [number, number] } | null {
+    if (!this._svg || !this._scales) return null;
+    const rect = this._svg.getBoundingClientRect();
+    const localX = clientX - rect.left;
+    const localY = clientY - rect.top;
+    const dataX = (localX - this._transform.x) / this._transform.k;
+    const dataY = (localY - this._transform.y) / this._transform.k;
+    const searchRadius = 15 / this._transform.k;
+    const nearest = this._quadtreeIndex.findNearest(dataX, dataY, searchRadius);
+    if (!nearest) return null;
+    if (this._getOpacity(nearest) === 0) return null;
+    if (this._webglRenderer && !this._webglRenderer.isPointRendered(nearest.id)) return null;
+    return { proteinId: nearest.id, dataCoords: [nearest.x, nearest.y] };
+  }
+
+  private _handleContextMenu(e: MouseEvent) {
+    const hit = this._hitTestAtClient(e.clientX, e.clientY);
+    if (!hit) {
+      this._contextMenuOpen = false;
+      return;
+    }
+    e.preventDefault();
+    const hasAccession = /^[A-Z][0-9][A-Z0-9]{3}[0-9]|^[A-Z]{2}_\d+/.test(hit.proteinId);
+    this._contextMenuItems = resolveMenuItems({ ...hit, hasAccession });
+    const rect = this.getBoundingClientRect();
+    this._contextMenuX = e.clientX - rect.left;
+    this._contextMenuY = e.clientY - rect.top;
+    this._contextMenuOpen = true;
+  }
+
+  private _handleContextMenuAction(e: CustomEvent<ContextMenuAction>) {
+    e.stopPropagation();
+    const { type, proteinId } = e.detail;
+    if (type === 'copy-id') {
+      void navigator.clipboard?.writeText(proteinId);
+    } else if (type === 'view-uniprot') {
+      window.open(`https://www.uniprot.org/uniprotkb/${proteinId}/entry`, '_blank', 'noopener');
+    }
+    this.dispatchEvent(
+      new CustomEvent('context-menu-action', {
+        detail: e.detail,
+        bubbles: true,
+        composed: true,
+      }),
+    );
+  }
+
+  private _handleContextMenuClose() {
+    this._contextMenuOpen = false;
+  }
+
   render() {
     const config = this._mergedConfig;
     const useAltCanvas = this._canvasKey % 2 === 1;
 
     return html`
-      <div class="container">
+      <div class="container" @contextmenu="${this._handleContextMenu}">
         <!-- Canvas for high-performance rendering (always visible for better performance) -->
         ${useAltCanvas
           ? html`<canvas
@@ -2117,6 +2177,14 @@ export class ProtspaceScatterplot extends LitElement {
               </div>
             `
           : ''}
+        <protspace-context-menu
+          style="position: absolute; left:${this._contextMenuX}px; top:${this
+            ._contextMenuY}px; z-index: 20;"
+          .open="${this._contextMenuOpen}"
+          .items="${this._contextMenuItems}"
+          @context-menu-action="${this._handleContextMenuAction}"
+          @context-menu-close="${this._handleContextMenuClose}"
+        ></protspace-context-menu>
       </div>
     `;
   }