SDC Constraints for digitally noise filtered CLOCK and DATA inputs
You have a logic clock of 50 MHz and a 1 MHz synchronous serial input consisting of CLK2 and DATAIN.
The function of the serial clock CLK2 is to indicate the timing for DATAIN as it travels across the serial bus. It is not to connect to the clock input of flip-flops in a logic circuit.
Your circuit should see serial CLK2 as a logic signal, just like DATAIN is. Serial CLK2 happens to be a square-wave control signal. At an agreed point within each serial CLK2 cycle, DATAIN will be steady and the data bit on it can be sampled. It is usually shifted into a shift register but you don't describe your application so I can't say.
Synchronous serial protocols reference their serial data stable periods and changing periods to an edge on their serial clock. Here, serial CLK2 is nice and slow compared to your logic clock CLK1, which has a 50:1 clock speed advantage over it. Your receiver needs to detect a rising or falling edge on serial CLK2 to find a reference point. This all takes place after your input filter circuit. A rising edge is a 1 from your CLK2 filter that was preceded by a 0, while the opposite is a falling edge.
Just to complete the picture, if a circuit has to sample synchronous serial data at a later phase of the serial clock period, it can detect the edge then delay by a number of logic clocks to reach a particular point in the serial clock cycle phase before taking a serial data bit. But it's unlikely you'll need that here.
Your input filter circuit is fine but the part beyond needs redesigning to meet these changes. Please remember that throughout your synchronous logic circuit, the only clock going to flip-flops or registers is logic clock CLK1. Do not clock anything from CLK2.
Your SDC file now doesn't need clock constraints on CLK2 because it isn't a circuit clock. It will need a constraint on each of CLK2 and DATAIN from the input pin to first register path delay, which you can find.