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 (
    5623, 5624, 5625, 5626, 5627, 5628, 5629, 
    5630, 5631, 5632, 5633, 5634, 5635, 
    5636, 5637, 5638, 5639, 5640, 5641, 
    5642, 5643, 5644, 5645, 5646, 5647, 
    5648, 5649, 5650, 5651, 5652, 5653, 
    5654, 5655, 5656, 5657, 5658, 5659, 
    5660, 5661, 5662, 5663, 5664, 5665, 
    5666, 5667, 3137, 1473, 1474
  ) 
  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 0.00092

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "34.06"
    },
    "grouping_operation": {
      "using_filesort": false,
      "table": {
        "table_name": "cscart_product_prices",
        "access_type": "range",
        "possible_keys": [
          "usergroup",
          "product_id",
          "lower_limit",
          "usergroup_id"
        ],
        "key": "product_id",
        "used_key_parts": [
          "product_id"
        ],
        "key_length": "3",
        "rows_examined_per_scan": 49,
        "rows_produced_per_join": 9,
        "filtered": "20.00",
        "index_condition": "(`gaseus`.`cscart_product_prices`.`product_id` in (5623,5624,5625,5626,5627,5628,5629,5630,5631,5632,5633,5634,5635,5636,5637,5638,5639,5640,5641,5642,5643,5644,5645,5646,5647,5648,5649,5650,5651,5652,5653,5654,5655,5656,5657,5658,5659,5660,5661,5662,5663,5664,5665,5666,5667,3137,1473,1474))",
        "cost_info": {
          "read_cost": "33.08",
          "eval_cost": "0.98",
          "prefix_cost": "34.06",
          "data_read_per_join": "235"
        },
        "used_columns": [
          "product_id",
          "price",
          "percentage_discount",
          "lower_limit",
          "usergroup_id"
        ],
        "attached_condition": "((`gaseus`.`cscart_product_prices`.`lower_limit` = 1) and (`gaseus`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}