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 (
    245, 238, 239, 74, 73, 71, 75, 72, 70, 76, 
    67, 86, 106, 105, 101, 69, 125, 120, 117, 
    113, 331, 335, 339, 341, 355, 356, 357, 
    358, 359, 360, 361, 362, 363, 364, 365, 
    366, 367, 368, 369, 370, 379, 380, 381, 
    382, 383, 384, 385, 386, 387, 388, 389, 
    390, 391, 392, 393, 394, 395, 396, 397, 
    398, 399, 400, 401, 402, 403, 404, 405, 
    406, 407, 408, 409, 410, 411, 412, 413, 
    414, 415, 416, 417, 418, 419, 420, 421, 
    422, 423, 424, 425, 426, 68
  ) 
  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 0.00109

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "258.45"
    },
    "grouping_operation": {
      "using_temporary_table": true,
      "using_filesort": true,
      "cost_info": {
        "sort_cost": "178.00"
      },
      "table": {
        "table_name": "cscart_product_prices",
        "access_type": "ALL",
        "possible_keys": [
          "usergroup",
          "product_id",
          "lower_limit",
          "usergroup_id"
        ],
        "rows_examined_per_scan": 383,
        "rows_produced_per_join": 178,
        "filtered": "46.48",
        "cost_info": {
          "read_cost": "44.86",
          "eval_cost": "35.60",
          "prefix_cost": "80.46",
          "data_read_per_join": "4K"
        },
        "used_columns": [
          "product_id",
          "price",
          "percentage_discount",
          "lower_limit",
          "usergroup_id"
        ],
        "attached_condition": "((`pankajecarter_systemfour`.`cscart_product_prices`.`lower_limit` = 1) and (`pankajecarter_systemfour`.`cscart_product_prices`.`product_id` in (245,238,239,74,73,71,75,72,70,76,67,86,106,105,101,69,125,120,117,113,331,335,339,341,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,68)) and (`pankajecarter_systemfour`.`cscart_product_prices`.`usergroup_id` in (0,1)))"
      }
    }
  }
}

Result

product_id price
67 339.99000000
68 799.99000000
69 529.99000000
70 499.99000000
71 529.99000000
72 599.99000000
73 589.99000000
74 524.99000000
75 489.99000000
76 439.99000000
86 359.00000000
101 188.88000000
105 169.99000000
106 179.99000000
113 449.99000000
117 729.99000000
120 199.99000000
125 149.99000000
238 499.99000000
239 509.99000000
245 699.00000000
331 1200.00000000
335 1200.00000000
339 1200.00000000
341 1200.00000000
355 10200.00000000
356 10200.00000000
357 1200.00000000
358 1200.00000000
359 1200.00000000
360 1200.00000000
361 1200.00000000
362 1200.00000000
363 10200.00000000
364 10200.00000000
365 1200.00000000
366 1200.00000000
367 1200.00000000
368 1200.00000000
369 1200.00000000
370 1200.00000000
379 1200.00000000
380 1200.00000000
381 1200.00000000
382 1200.00000000
383 1200.00000000
384 1200.00000000
385 1200.00000000
386 1200.00000000
387 1200.00000000
388 1200.00000000
389 1200.00000000
390 1200.00000000
391 1200.00000000
392 1200.00000000
393 1200.00000000
394 1200.00000000
395 1200.00000000
396 1200.00000000
397 1200.00000000
398 1200.00000000
399 1200.00000000
400 1200.00000000
401 1200.00000000
402 1200.00000000
403 1200.00000000
404 1200.00000000
405 1200.00000000
406 1200.00000000
407 1200.00000000
408 1200.00000000
409 1200.00000000
410 1200.00000000
411 1200.00000000
412 1200.00000000
413 1200.00000000
414 1200.00000000
415 1200.00000000
416 1200.00000000
417 1200.00000000
418 1200.00000000
419 1200.00000000
420 1200.00000000
421 1200.00000000
422 1200.00000000
423 1200.00000000
424 1200.00000000
425 1200.00000000
426 1200.00000000