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 (
    6952, 6953, 6947, 3430, 3429, 3437, 3436, 
    3438, 6959, 3425, 6958, 6960, 6968, 
    6961, 6964, 6957, 6956, 6954, 6955, 
    3500, 3501, 3431, 6948, 3499, 3455, 
    3466, 3454, 3456, 3449, 3461, 3441, 
    3444, 3471, 3442, 3480, 3448, 3440, 
    3467, 3468, 3435, 3476, 3447, 3439, 
    3465, 3446, 3460, 3443, 3469
  ) 
  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": "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": "19.99",
        "index_condition": "(`test2_gaseus`.`cscart_product_prices`.`product_id` in (6952,6953,6947,3430,3429,3437,3436,3438,6959,3425,6958,6960,6968,6961,6964,6957,6956,6954,6955,3500,3501,3431,6948,3499,3455,3466,3454,3456,3449,3461,3441,3444,3471,3442,3480,3448,3440,3467,3468,3435,3476,3447,3439,3465,3446,3460,3443,3469))",
        "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": "((`test2_gaseus`.`cscart_product_prices`.`lower_limit` = 1) and (`test2_gaseus`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}