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 (
    339776, 339474, 339552, 339649, 339743, 
    339756, 339647, 339665, 339470, 339773, 
    339577, 339848, 339703, 339749, 339669, 
    339455, 339666, 339789, 339651, 339565, 
    339544, 339626, 339670, 339543, 339646, 
    339824, 339833, 339834, 339575, 339784, 
    339698, 339830, 339631, 339628, 339662, 
    339767, 339557, 339567, 339549, 339595, 
    339823, 339673, 339853, 339658, 339717, 
    339763, 339852, 339542, 339818, 339653, 
    339487, 339822, 339472, 339613, 339682, 
    339480, 339555, 339639, 339560, 339579, 
    339680, 339559, 339788, 339850, 339854, 
    339815, 339772, 339561, 339785, 339766, 
    339475, 339688, 339566, 339661, 339558, 
    339819, 339585, 339837, 339563, 339640, 
    339568, 339790, 339578, 339634, 339598, 
    339629, 339672, 339546, 339844, 339641, 
    339832, 339840, 339624, 339627, 339687, 
    339842, 339612, 339827, 339642, 339800
  ) 
  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 0.00192

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "280.31"
    },
    "grouping_operation": {
      "using_filesort": false,
      "table": {
        "table_name": "cscart_product_prices",
        "access_type": "range",
        "possible_keys": [
          "usergroup",
          "product_id",
          "lower_limit",
          "usergroup_id"
        ],
        "key": "usergroup",
        "used_key_parts": [
          "product_id",
          "usergroup_id",
          "lower_limit"
        ],
        "key_length": "9",
        "rows_examined_per_scan": 200,
        "rows_produced_per_join": 200,
        "filtered": "100.00",
        "cost_info": {
          "read_cost": "240.31",
          "eval_cost": "40.00",
          "prefix_cost": "280.31",
          "data_read_per_join": "12K"
        },
        "used_columns": [
          "product_id",
          "price",
          "percentage_discount",
          "lower_limit",
          "usergroup_id"
        ],
        "attached_condition": "((`webmarco`.`cscart_product_prices`.`lower_limit` = 1) and (`webmarco`.`cscart_product_prices`.`product_id` in (339776,339474,339552,339649,339743,339756,339647,339665,339470,339773,339577,339848,339703,339749,339669,339455,339666,339789,339651,339565,339544,339626,339670,339543,339646,339824,339833,339834,339575,339784,339698,339830,339631,339628,339662,339767,339557,339567,339549,339595,339823,339673,339853,339658,339717,339763,339852,339542,339818,339653,339487,339822,339472,339613,339682,339480,339555,339639,339560,339579,339680,339559,339788,339850,339854,339815,339772,339561,339785,339766,339475,339688,339566,339661,339558,339819,339585,339837,339563,339640,339568,339790,339578,339634,339598,339629,339672,339546,339844,339641,339832,339840,339624,339627,339687,339842,339612,339827,339642,339800)) and (`webmarco`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}