I know villain pretty well we are on friendly terms....we both have history together

this is like 0.15/0.30 USD close around that Villain and me are the two biggest stacks

OTTH

PokerStars Hand #201716921974: Hold'em No Limit (Rs.*10/Rs.*25 INR) - 2019/06/25 6:43:08 ET
Table 'Giomus II' 6-max Seat #6 is the button
Seat 1: V2 (Rs.*925 in chips)
Seat 3: Hero (Rs.*4663.83 in chips)
Seat 5: Villain (Rs.*5307.55 in chips)
Seat 6: V3 (Rs.*2430 in chips)
V3: posts small blind Rs.*10
Hero: posts big blind Rs.*25
*** HOLE CARDS ***
Dealt to Hero [2s 2h]
Villain: calls Rs.*25
V3: folds
V2: folds
Hero: checks
*** FLOP *** [Kc 5s 2c]
Hero: checks
Villain: checks
*** TURN *** [Kc 5s 2c] [7s]
Hero: bets Rs.*56.91
Villain: calls Rs.*56.91
*** RIVER *** [Kc 5s 2c 7s] [4s]
Hero: bets Rs.*82.44
Villain: raises Rs.*82.44 to Rs.*164.88

Hero: calls Rs.*82.44
*** SHOW DOWN ***
Villain: shows [5d Ah] (a pair of Fives)
Hero: shows [2s 2h] (three of a kind, Deuces)
Hero collected Rs.*477.65 from pot
*** SUMMARY ***
Total pot Rs.*503.58 | Rake Rs.*25.93
Board [Kc 5s 2c 7s 4s]
Seat 1: V2 (small blind) folded before Flop
Seat 3: Hero (big blind) showed [2s 2h] and won (Rs.*477.65) with three of a kind, Deuces
Seat 5: Villain showed [5d Ah] and lost with a pair of Fives
Seat 6: V3 (button) folded before Flop (didn't bet)

The river actually grossed me out.....the backdoor flush gets there and even hands like A3cc or A3ss have me smoked.

as played did I miss out on value ?

This hand history is hard to read, but calling his river raise is fine. I don't think you can justify a re-raise - especially since the flush got there.

Unless you have prior reads on the villain . . .

Miss out on value? You think your 3b otr gets called by 5s? Villain was bluffing and probably only calls with a flush. You got exactly the most value you're going to get, EXCEPT you should have bet the flop. Think about it. Villain called pre from equivalent of co. He won't have KK or 55 (usually). You have all the K5, K2, 52, 55, 22 (nut advantage). You also have more hands that connect with this flop (43, 64, 63). You probably have more A highs too. So you likely have the range advantage. So bet. Bet small. Then you'll get a little more value, but v helped you out a lot with his bluff raise otr.