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 (
    339487, 339682, 339613, 339639, 339555, 
    339480, 339560, 271697, 339579, 339854, 
    339680, 339559, 339788, 339850, 339772, 
    339475, 339815, 339785, 339561, 339566, 
    339766, 339558, 339568, 339688, 339661, 
    339563, 339819, 339837, 339640, 339585, 
    339790, 339598, 339634, 381694, 339578, 
    339546, 339629, 392159, 339672, 381692, 
    339844, 339641, 339624, 339832, 339627, 
    339840, 381689, 339687, 381685, 220162, 
    339842, 339612, 339800, 339642, 339827, 
    265036, 339764, 339605, 339564, 220170, 
    431190, 339690, 339462, 381682, 430574, 
    339562, 339663, 339793, 339554, 339700, 
    271696, 392172, 271695, 431092, 339792, 
    381688, 431106, 435505, 339811, 381693, 
    381691, 220169, 431147, 339801, 339459, 
    339590, 339473, 339592, 430849, 220166, 
    339799, 339679, 381690, 339791, 339795, 
    339660, 339623, 339803, 339813, 339659
  ) 
  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 0.00157

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 (339487,339682,339613,339639,339555,339480,339560,271697,339579,339854,339680,339559,339788,339850,339772,339475,339815,339785,339561,339566,339766,339558,339568,339688,339661,339563,339819,339837,339640,339585,339790,339598,339634,381694,339578,339546,339629,392159,339672,381692,339844,339641,339624,339832,339627,339840,381689,339687,381685,220162,339842,339612,339800,339642,339827,265036,339764,339605,339564,220170,431190,339690,339462,381682,430574,339562,339663,339793,339554,339700,271696,392172,271695,431092,339792,381688,431106,435505,339811,381693,381691,220169,431147,339801,339459,339590,339473,339592,430849,220166,339799,339679,381690,339791,339795,339660,339623,339803,339813,339659)) and (`webmarco`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}