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 (
    3354, 3834, 3308, 3306, 3841, 3212, 3226, 
    3350, 3218, 3392, 3301, 3751, 3828, 
    3520, 3529, 3809, 3518, 3918, 3215, 
    3213, 3597, 3752, 3552, 3836, 3232, 
    3589, 3556, 3845, 3822, 3370, 3843, 
    3840, 3882, 3377, 3373, 3593, 3551, 
    3831, 3519, 3919, 3356, 3404, 3366, 
    3222, 3522, 3401, 3358, 3537, 3291, 
    3225, 3844, 3876, 3559, 3917, 3528, 
    3819, 3922, 3534, 3531, 3812, 3372, 
    3374, 3309, 3590, 3351, 3532, 3546, 
    3827, 3548, 3521, 3355, 3398, 3357, 
    3369, 3807, 3525, 3408, 3746, 3393, 
    3744
  ) 
  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 0.00266

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "56.01"
    },
    "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": 80,
        "rows_produced_per_join": 15,
        "filtered": "19.99",
        "index_condition": "(`softwarepirmam_hewadelivard_cscart_4`.`cscart_product_prices`.`product_id` in (3354,3834,3308,3306,3841,3212,3226,3350,3218,3392,3301,3751,3828,3520,3529,3809,3518,3918,3215,3213,3597,3752,3552,3836,3232,3589,3556,3845,3822,3370,3843,3840,3882,3377,3373,3593,3551,3831,3519,3919,3356,3404,3366,3222,3522,3401,3358,3537,3291,3225,3844,3876,3559,3917,3528,3819,3922,3534,3531,3812,3372,3374,3309,3590,3351,3532,3546,3827,3548,3521,3355,3398,3357,3369,3807,3525,3408,3746,3393,3744))",
        "cost_info": {
          "read_cost": "54.41",
          "eval_cost": "1.60",
          "prefix_cost": "56.01",
          "data_read_per_join": "383"
        },
        "used_columns": [
          "product_id",
          "price",
          "percentage_discount",
          "lower_limit",
          "usergroup_id"
        ],
        "attached_condition": "((`softwarepirmam_hewadelivard_cscart_4`.`cscart_product_prices`.`lower_limit` = 1) and (`softwarepirmam_hewadelivard_cscart_4`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}