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 (
    3826, 3660, 3649, 3733, 3740, 3743, 3944, 
    3741, 3811, 3441, 3653, 3946, 3768, 
    3734, 3821, 3747, 3641, 3952, 3738, 
    3435, 3798, 3443, 3730, 3737, 3638, 
    3655, 3729, 3658, 3851, 3668, 3942, 
    3732, 3448, 3702, 3728, 3852, 3850, 
    3731, 3769, 3642, 3745, 3943, 3623, 
    3670, 3684, 3645, 3437, 3637, 3682, 
    3767, 3950, 3644, 3659, 3766, 3864, 
    3940, 3436, 3739, 3444, 3785, 3442, 
    3787, 3945, 3438, 3770, 3865, 3447, 
    3793, 3450, 3772, 3795, 3788, 3439, 
    3446, 3687, 3860, 3794, 3858, 3869, 
    3948, 3449, 3941, 3871, 3786, 3853, 
    3857, 3863, 3867, 3951, 3862, 3854, 
    3949, 3727, 3699, 3881, 3855, 3859
  ) 
  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 0.00248

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "67.91"
    },
    "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": 97,
        "rows_produced_per_join": 19,
        "filtered": "19.99",
        "index_condition": "(`softwarepirmam_hewadelivard_cscart_4`.`cscart_product_prices`.`product_id` in (3826,3660,3649,3733,3740,3743,3944,3741,3811,3441,3653,3946,3768,3734,3821,3747,3641,3952,3738,3435,3798,3443,3730,3737,3638,3655,3729,3658,3851,3668,3942,3732,3448,3702,3728,3852,3850,3731,3769,3642,3745,3943,3623,3670,3684,3645,3437,3637,3682,3767,3950,3644,3659,3766,3864,3940,3436,3739,3444,3785,3442,3787,3945,3438,3770,3865,3447,3793,3450,3772,3795,3788,3439,3446,3687,3860,3794,3858,3869,3948,3449,3941,3871,3786,3853,3857,3863,3867,3951,3862,3854,3949,3727,3699,3881,3855,3859))",
        "cost_info": {
          "read_cost": "65.97",
          "eval_cost": "1.94",
          "prefix_cost": "67.91",
          "data_read_per_join": "465"
        },
        "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)))"
      }
    }
  }
}