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 (
    3489, 3492, 3496, 3490, 3494, 6951, 3502, 
    3503, 3493, 3498, 3428, 3433, 3432, 
    22, 23, 24, 3933, 3934, 3935, 1334, 1335, 
    1336, 1337, 1338, 1339, 1340, 1341, 
    1342, 1343, 1344, 1355, 1356, 1357, 
    1358, 1359, 1360, 1361, 1362, 1363, 
    1364, 3688, 3689, 3690, 3691, 3692, 
    3693, 3694, 3695, 3696, 3697, 3709, 
    3710, 3711, 3712, 3713, 3714, 3715, 
    3716, 3717, 3718, 3708, 3152, 25, 1365, 
    3138, 3149, 6719, 3146, 3150, 1345, 
    1346, 1347, 1348, 1349, 1350, 1351, 
    1352, 1353, 1354, 3698, 3699, 3700, 
    3701, 3702, 3703, 3704, 3705, 3706, 
    3707, 6723, 6717, 6720, 3151, 3864, 
    3145, 6721
  ) 
  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 0.00195

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "67.21"
    },
    "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": 96,
        "rows_produced_per_join": 19,
        "filtered": "20.00",
        "index_condition": "(`gaseus`.`cscart_product_prices`.`product_id` in (3489,3492,3496,3490,3494,6951,3502,3503,3493,3498,3428,3433,3432,22,23,24,3933,3934,3935,1334,1335,1336,1337,1338,1339,1340,1341,1342,1343,1344,1355,1356,1357,1358,1359,1360,1361,1362,1363,1364,3688,3689,3690,3691,3692,3693,3694,3695,3696,3697,3709,3710,3711,3712,3713,3714,3715,3716,3717,3718,3708,3152,25,1365,3138,3149,6719,3146,3150,1345,1346,1347,1348,1349,1350,1351,1352,1353,1354,3698,3699,3700,3701,3702,3703,3704,3705,3706,3707,6723,6717,6720,3151,3864,3145,6721))",
        "cost_info": {
          "read_cost": "65.29",
          "eval_cost": "1.92",
          "prefix_cost": "67.21",
          "data_read_per_join": "460"
        },
        "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)))"
      }
    }
  }
}