Regarding the point in the question, of:
what's the point of the whole court system if no body have to obey its decision?
One should realize that the Torah describes a legal system within a functioning country. One wouldn't ask what the point is of the whole U.S. Court system if there is no mitzvah to obey? The courts in the U.S. have teeth.
So did the Biblical courts.
In Devarim 16:18, the very first pasuk of parashat Shofetim:
שֹׁפְטִים וְשֹׁטְרִים תִּתֶּן לְךָ בְּכָל שְׁעָרֶיךָ אֲשֶׁר יְהֹוָה אֱלֹהֶיךָ נֹתֵן לְךָ לִשְׁבָטֶיךָ וְשָׁפְטוּ אֶת הָעָם מִשְׁפַּט צֶדֶק:
You shall set up judges and law enforcement officials for yourself in all your cities that the Lord, your God, is giving you, for your tribes, and they shall judge the people [with] righteous judgment.
The Shofetim are the judges and the Shoterim are the law enforcement officials. As Rashi there explains:
"Judges and law-enforcement officials: Heb. שֹׁפְטִים וְשֹׁטְרִים. שֹׁפְטִים are judges who decide the verdict, and שֹׁטְרִים are those who chastise the people in compliance with their order, (who strike and bind [not found in early editions]) with rods and straps, until he [the guilty party] accepts the judge’s verdict."
How this translates to a time / place when the court is not the law of the land is another question. This article lays out some of the teeth that a modern bet din may have.
The verse (Devarim 17:12) cited in the other answer, with the associated capital punishment, refers to a rebellious elder who rules to act not in accordance with the Sanhedrin (High Court), and so does not refer to a litigant who merely disagrees with a court verdict and refuses to comply. Note pasuk 8 which begins כִּי יִפָּלֵא מִמְּךָ דָבָר לַמִּשְׁפָּט. Perhaps one of the slightly earlier verses in context -- though those are also parsed to refer to the rebellious elder case -- is also taken as an instruction to listen in practical action to the bet din (or at least the High Court), e.g. pasuk 10, וְעָשִׂיתָ עַל פִּי הַדָּבָר אֲשֶׁר יַגִּידוּ לְךָ.
Avot 1:8 meanwhile indicates that it is accepting the verdict that renders one blameless:
יהודה בן טבאי ושמעון בן שטח קיבלו מהם. יהודה בן טבאי אומר, אל תעש עצמך כעורכי הדיינים. וכשיהיו בעלי הדין עומדין לפניך, יהיו בעיניך כרשעים; וכשנפטרים מלפניך, יהיו בעיניך כזכאים, שקיבלו עליהן את הדין.
When the litigants are before you, they should be in your eyes as evildoers [such that you should carefully weigh what they say and not take them at their mere words] and when they leave from before you, they should be in your eyes as blameless, for they have accepted upon themselves the law.