SELECT 
  cscart_product_prices.product_id, 
  MIN(
    IF(
      cscart_product_prices.percentage_discount = 0, 
      cscart_product_prices.price, 
      cscart_product_prices.price - (
        cscart_product_prices.price * cscart_product_prices.percentage_discount
      )/ 100
    )
  ) AS price 
FROM 
  cscart_product_prices 
WHERE 
  cscart_product_prices.product_id IN (
    3866, 3867, 3868, 3869, 3865, 3870, 3872, 
    3871, 3876, 3862, 3863, 35730, 3864, 
    3861, 35731, 3873, 47984, 3874, 3884, 
    3875, 3880, 3877, 3859, 3879, 35729, 
    3881, 3860, 3883, 3882, 35859
  ) 
  AND cscart_product_prices.lower_limit = 1 
  AND cscart_product_prices.usergroup_id IN (0, 1) 
GROUP BY 
  cscart_product_prices.product_id

Query time 0.00648

JSON explain

{
  "query_block": {
    "select_id": 1,
    "nested_loop": [
      {
        "table": {
          "table_name": "cscart_product_prices",
          "access_type": "range",
          "possible_keys": [
            "usergroup",
            "product_id",
            "lower_limit",
            "usergroup_id"
          ],
          "key": "product_id",
          "key_length": "3",
          "used_key_parts": ["product_id"],
          "rows": 30,
          "filtered": 99.9960556,
          "index_condition": "cscart_product_prices.product_id in (3866,3867,3868,3869,3865,3870,3872,3871,3876,3862,3863,35730,3864,3861,35731,3873,47984,3874,3884,3875,3880,3877,3859,3879,35729,3881,3860,3883,3882,35859)",
          "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.usergroup_id in (0,1)"
        }
      }
    ]
  }
}