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 (
    430838, 431063, 430904, 430909, 431008, 
    431183, 339599, 430695, 431159, 339845, 
    339816, 430815, 430832, 430914, 339723, 
    430939, 339582, 431356, 430880, 430891, 
    431197, 430893, 430913, 430923, 431135, 
    339839, 430662, 430930, 431089, 431136, 
    339486, 381712, 381704, 430676, 430787, 
    430847, 430980, 431078, 431226, 431393, 
    430854, 430806, 431142, 430672, 430633, 
    430760, 430869, 431119, 431174, 430829, 
    430976, 431111, 431327, 430844, 431123, 
    431325, 339727, 339594, 430644, 430772, 
    431031, 430663, 430899, 430981, 431023, 
    431088, 339765, 430753, 430845, 431245, 
    430796, 430801, 430876, 430958, 431032, 
    431093, 431238, 431467, 430712, 430884, 
    431062, 431251, 339762, 430898, 431121, 
    431167, 430851, 430698, 430927, 430730, 
    431291, 431423, 430651, 431314, 339691, 
    430883, 381713, 430685, 430722, 430809
  ) 
  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 0.00225

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 (430838,431063,430904,430909,431008,431183,339599,430695,431159,339845,339816,430815,430832,430914,339723,430939,339582,431356,430880,430891,431197,430893,430913,430923,431135,339839,430662,430930,431089,431136,339486,381712,381704,430676,430787,430847,430980,431078,431226,431393,430854,430806,431142,430672,430633,430760,430869,431119,431174,430829,430976,431111,431327,430844,431123,431325,339727,339594,430644,430772,431031,430663,430899,430981,431023,431088,339765,430753,430845,431245,430796,430801,430876,430958,431032,431093,431238,431467,430712,430884,431062,431251,339762,430898,431121,431167,430851,430698,430927,430730,431291,431423,430651,431314,339691,430883,381713,430685,430722,430809)) and (`webmarco`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}