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 (
    1154, 3315, 3318, 3687, 5076, 4691, 3071, 
    513, 3505, 3319, 3306, 3296, 1172, 1173, 
    4917, 4918, 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, 3464, 3459, 6950, 3470, 3457, 
    3462, 3450, 3458, 3463, 3451, 3445, 
    3472, 3481, 3482, 3475, 3483, 3474, 
    3473, 3426, 6949, 3427, 3477, 3452, 
    3478, 3479, 3453, 3491, 3488, 3497, 
    3495, 3489, 3492, 3496, 3490, 3494, 
    6951, 3502, 3503, 3493, 3498, 3428, 
    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 0.00212

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "61.36"
    },
    "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": 88,
        "rows_produced_per_join": 17,
        "filtered": "20.00",
        "index_condition": "(`gaseus`.`cscart_product_prices`.`product_id` in (1154,3315,3318,3687,5076,4691,3071,513,3505,3319,3306,3296,1172,1173,4917,4918,3500,3501,3431,6948,3499,3455,3466,3454,3456,3449,3461,3441,3444,3471,3442,3480,3448,3440,3467,3468,3435,3476,3447,3439,3465,3446,3460,3443,3469,3464,3459,6950,3470,3457,3462,3450,3458,3463,3451,3445,3472,3481,3482,3475,3483,3474,3473,3426,6949,3427,3477,3452,3478,3479,3453,3491,3488,3497,3495,3489,3492,3496,3490,3494,6951,3502,3503,3493,3498,3428,5802))",
        "cost_info": {
          "read_cost": "59.60",
          "eval_cost": "1.76",
          "prefix_cost": "61.36",
          "data_read_per_join": "422"
        },
        "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)))"
      }
    }
  }
}