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 (
    47613, 3288, 28159, 3287, 3286, 3872, 
    1401, 3021, 6093, 4367, 5455, 36781, 
    2280, 3402, 1285, 2870, 36834, 5461, 
    5958, 5476, 1205, 5959, 5457, 5472, 
    5462, 2868, 31734, 5960, 5957, 5961, 
    5467, 35733
  ) 
  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 0.00294

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": 32,
          "filtered": 99.9960556,
          "index_condition": "cscart_product_prices.product_id in (47613,3288,28159,3287,3286,3872,1401,3021,6093,4367,5455,36781,2280,3402,1285,2870,36834,5461,5958,5476,1205,5959,5457,5472,5462,2868,31734,5960,5957,5961,5467,35733)",
          "attached_condition": "cscart_product_prices.lower_limit = 1 and cscart_product_prices.usergroup_id in (0,1)"
        }
      }
    ]
  }
}