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 (
    6843, 6840, 6841, 6846, 3430, 3429, 3437, 
    3436, 3438, 3477, 3452, 3478, 3479, 
    3453, 3491, 3488, 3497, 3495, 3489, 
    3492, 3496, 3490, 3494, 6951, 3502, 
    3503, 3493, 3498, 3428, 3419, 3418, 
    6946, 6945, 3411, 3415, 3417, 6942, 
    3410, 3413, 3416, 6940, 3414, 6938, 
    6941, 6944, 3412, 6937, 6939, 6943, 
    3165, 3139, 3140, 6712, 6713, 5802
  ) 
  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 0.00145

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "38.96"
    },
    "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": 56,
        "rows_produced_per_join": 11,
        "filtered": "20.00",
        "index_condition": "(`gaseus`.`cscart_product_prices`.`product_id` in (6843,6840,6841,6846,3430,3429,3437,3436,3438,3477,3452,3478,3479,3453,3491,3488,3497,3495,3489,3492,3496,3490,3494,6951,3502,3503,3493,3498,3428,3419,3418,6946,6945,3411,3415,3417,6942,3410,3413,3416,6940,3414,6938,6941,6944,3412,6937,6939,6943,3165,3139,3140,6712,6713,5802))",
        "cost_info": {
          "read_cost": "37.84",
          "eval_cost": "1.12",
          "prefix_cost": "38.96",
          "data_read_per_join": "268"
        },
        "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)))"
      }
    }
  }
}