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 (
    9953, 9942, 9676, 9932, 9937, 9573, 9574, 
    9575, 9576, 9577, 9672, 9578, 9638, 
    9643, 9671, 9581, 9582, 9584, 9585, 
    8687, 9685, 9954, 9681, 9682, 9955, 
    9683, 9686, 9956, 9758, 9612, 9730, 
    9616, 8933, 9732, 9735, 9587, 9589, 
    9599, 8936, 9565, 9600, 9604, 9606, 
    9947, 9621, 9610, 8939, 9611, 9664, 
    9665, 9748, 9564, 9750, 9623, 9958, 
    9960, 9666, 9952, 9959, 9949, 9753, 
    9944, 9754, 9562, 9756, 8983, 9673, 
    9961, 9957, 9757, 9626, 9627, 9629, 
    9630, 9632, 9633, 9635, 9640, 9945, 
    9950, 9641, 8945, 9625, 9645, 9647, 
    9677, 9648, 9650, 9921, 8941, 9922, 
    9923, 9925, 9924, 9745, 9651, 9652, 
    9746, 9654, 9926
  ) 
  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 0.01210

JSON explain

{
  "query_block": {
    "select_id": 1,
    "filesort": {
      "sort_key": "cscart_product_prices.product_id",
      "temporary_table": {
        "nested_loop": [
          {
            "table": {
              "table_name": "cscart_product_prices",
              "access_type": "ref",
              "possible_keys": [
                "usergroup",
                "product_id",
                "lower_limit",
                "usergroup_id"
              ],
              "key": "lower_limit",
              "key_length": "3",
              "used_key_parts": ["lower_limit"],
              "ref": ["const"],
              "rows": 11706,
              "filtered": 100,
              "attached_condition": "cscart_product_prices.lower_limit <=> 1 and cscart_product_prices.product_id in (9953,9942,9676,9932,9937,9573,9574,9575,9576,9577,9672,9578,9638,9643,9671,9581,9582,9584,9585,8687,9685,9954,9681,9682,9955,9683,9686,9956,9758,9612,9730,9616,8933,9732,9735,9587,9589,9599,8936,9565,9600,9604,9606,9947,9621,9610,8939,9611,9664,9665,9748,9564,9750,9623,9958,9960,9666,9952,9959,9949,9753,9944,9754,9562,9756,8983,9673,9961,9957,9757,9626,9627,9629,9630,9632,9633,9635,9640,9945,9950,9641,8945,9625,9645,9647,9677,9648,9650,9921,8941,9922,9923,9925,9924,9745,9651,9652,9746,9654,9926) and cscart_product_prices.usergroup_id in (0,1)"
            }
          }
        ]
      }
    }
  }
}