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 (
    6946, 6945, 3411, 3415, 3417, 6942, 3410, 
    3413, 3416, 6940, 3414, 6938, 6941, 
    6944, 3412, 6937, 6939, 6943, 3165, 
    3139, 3140, 6712, 6713, 3135, 5802, 
    6970, 6971, 6972, 6973, 6974, 6975, 
    3403, 3404, 3405, 3406, 3408, 3409, 
    6930, 6931, 6932, 6933, 6934, 6935, 
    6936, 3407, 2666, 3845, 2667
  ) 
  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 0.00105

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "33.61"
    },
    "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": 48,
        "rows_produced_per_join": 9,
        "filtered": "20.00",
        "index_condition": "(`gaseus`.`cscart_product_prices`.`product_id` in (6946,6945,3411,3415,3417,6942,3410,3413,3416,6940,3414,6938,6941,6944,3412,6937,6939,6943,3165,3139,3140,6712,6713,3135,5802,6970,6971,6972,6973,6974,6975,3403,3404,3405,3406,3408,3409,6930,6931,6932,6933,6934,6935,6936,3407,2666,3845,2667))",
        "cost_info": {
          "read_cost": "32.65",
          "eval_cost": "0.96",
          "prefix_cost": "33.61",
          "data_read_per_join": "230"
        },
        "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)))"
      }
    }
  }
}