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 (
    47488, 47234, 47232, 51280, 47452, 47248, 
    47058, 51278, 47051, 47046, 47045, 
    47044, 47043, 47042, 47041, 47040, 
    47039, 47038, 47037, 47036, 47035, 
    47034, 47235, 47115, 47113, 47112, 
    47111, 47110, 47109, 47108, 47107, 
    47106, 47105, 47104, 47103, 47102, 
    47101, 46931, 46946, 46945, 46944, 
    47214, 47213, 47212, 47211, 47210, 
    47209, 47208, 47207, 47206, 47205, 
    47204, 47203, 47202, 47201, 47200, 
    47199, 47196, 46936, 46876, 46875, 
    46918, 46785, 46746, 46943, 46942, 
    46941, 46940, 46910, 46703, 47010, 
    47009, 47008, 46935, 46929, 46928, 
    46927, 46926, 46688, 46925
  ) 
  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 0.00182

Explain
id select_type table type possible_keys key key_len ref rows Extra
1 SIMPLE cscart_product_prices range usergroup,product_id,lower_limit,usergroup_id usergroup 9 160 Using where

Result

product_id price
46688 1.69000000
46703 1.69000000
46746 1.69000000
46785 1.69000000
46875 1.69000000
46876 1.69000000
46910 1.69000000
46918 1.69000000
46925 1.69000000
46926 1.69000000
46927 1.69000000
46928 1.69000000
46929 1.69000000
46931 1.69000000
46935 1.69000000
46936 1.69000000
46940 1.69000000
46941 1.69000000
46942 1.69000000
46943 1.69000000
46944 1.69000000
46945 1.69000000
46946 1.69000000
47008 1.69000000
47009 1.69000000
47010 1.69000000
47034 1.69000000
47035 1.69000000
47036 1.69000000
47037 1.69000000
47038 1.69000000
47039 1.69000000
47040 1.69000000
47041 1.69000000
47042 1.69000000
47043 1.69000000
47044 1.69000000
47045 1.69000000
47046 1.69000000
47051 1.69000000
47058 1.69000000
47101 1.69000000
47102 1.69000000
47103 1.69000000
47104 1.69000000
47105 1.69000000
47106 1.69000000
47107 1.69000000
47108 1.69000000
47109 1.69000000
47110 1.69000000
47111 1.69000000
47112 1.69000000
47113 1.69000000
47115 1.69000000
47196 1.69000000
47199 1.69000000
47200 1.69000000
47201 1.69000000
47202 1.69000000
47203 1.69000000
47204 1.69000000
47205 1.69000000
47206 1.69000000
47207 1.69000000
47208 1.69000000
47209 1.69000000
47210 1.69000000
47211 1.69000000
47212 1.69000000
47213 1.69000000
47214 1.69000000
47232 1.69000000
47234 1.69000000
47235 1.69000000
47248 1.69000000
47452 1.69000000
47488 1.69000000
51278 1.69000000
51280 1.69000000