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 (
    16150, 15902, 16716, 16813, 16812, 16849, 
    17017, 16845, 16932, 16888, 16889, 
    15798, 16861, 16862, 16943, 15835, 
    15836, 15839, 15834, 15837, 16881, 
    15844, 16929, 16938, 16937, 16152, 
    16153, 16947, 15912, 15913, 15797, 
    13030, 13029, 15832, 16801, 16798, 
    16800, 16946, 16827, 16826, 16871, 
    16858, 15845, 16345, 15910, 16941, 
    16940, 16939
  ) 
  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 0.00138

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "66.01"
    },
    "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": 120,
        "rows_produced_per_join": 17,
        "filtered": "14.40",
        "index_condition": "(`dev_yourmart_co_bw`.`cscart_product_prices`.`product_id` in (16150,15902,16716,16813,16812,16849,17017,16845,16932,16888,16889,15798,16861,16862,16943,15835,15836,15839,15834,15837,16881,15844,16929,16938,16937,16152,16153,16947,15912,15913,15797,13030,13029,15832,16801,16798,16800,16946,16827,16826,16871,16858,15845,16345,15910,16941,16940,16939))",
        "cost_info": {
          "read_cost": "64.28",
          "eval_cost": "1.73",
          "prefix_cost": "66.01",
          "data_read_per_join": "414"
        },
        "used_columns": [
          "product_id",
          "price",
          "percentage_discount",
          "lower_limit",
          "usergroup_id"
        ],
        "attached_condition": "((`dev_yourmart_co_bw`.`cscart_product_prices`.`lower_limit` = 1) and (`dev_yourmart_co_bw`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}