How to fix shift key animation only when tool is equipped?

To determine if the tool is equipped or not, there are two events that belong to the Tool class.

The first being Tool.Equipped. This event fires when a tool is equipped by a player.

The second is Tool.Unequipped. This event fires when a tool is unequipped by a player.

A way you could incorporate these events into your code is:

-- Services
local userInputService = game:GetService("UserInputService")
local playersService = game:GetService("Players")

local Player = game.Players.LocalPlayer
local Character = Player.Character or Player.CharacterAdded:Wait()

local sp = script.Parent

-- Variables
local player = playersService.LocalPlayer
local character = player.Character or player.CharacterAdded:Wait()
local humanoid = character:WaitForChild("Humanoid")
local pcButton = Enum.KeyCode.LeftShift
local xboxButton = Enum.KeyCode.ButtonL3
local IsEquipped = false

local tool = -- location of tool

-- Animation
local animation = script:WaitForChild("SprintAnim")
local sprintTrack = humanoid:LoadAnimation(animation)

-- Input controller
userInputService.InputBegan:Connect(function(input, processed)
    if input.KeyCode == (pcButton or xboxButton) and not processed and IsEquipped then
        sprintTrack:Play(.1)
    end
end)

userInputService.InputEnded:Connect(function(input, processed)
    if input.KeyCode == (pcButton or xboxButton) and not processed then
        sprintTrack:Stop(.1)
    end
end)

--Character.ChildRemoved:Connect(function(RemovedChild)
--    if RemovedChild:IsA("Tool") then
--        sprintTrack:Stop(0)
--        --the tool is unequipped
--        --RemovedChild is the tool unequipped
--    end
--end)

tool.Equipped:Connect(function()
	IsEquipped = true
end)

tool.Unequipped:Connect(function()
	IsEquipped = false
	sprintTrack:Stop(0)
end)