Bode W, Turk D, Stürzebecher J
Max-Planck-Institut für Biochemie, Martinsried, Federal Republic of Germany.
Eur J Biochem. 1990 Oct 5;193(1):175-82. doi: 10.1111/j.1432-1033.1990.tb19320.x.
The X-ray crystal structure of the trypsin complex formed with N alpha-(2-naphthyl-sulphonyl-glycyl)-DL-p-amidinophenylalanyl-piper idine (NAPAP) was determined with X-ray data to 0.18-nm resolution and crystallographically refined. NAPAP binds into the active site of trypsin in a quite compact form: the p-amidinophenylalanine moiety of the D-stereoisomer binds into the specificity pocket; the glycyl group is hydrogen bonded with Gly216; the naphthyl group stands perpendicular to the indole moiety of Trp215; the piperidine ring is tightly packed between this naphthyl moiety and His57; in consequence the carboxy-terminal amido bond of NAPAP is located in such a way that it is not susceptible to the active-site Ser195. NAPAP and (2R,4R)-4-methyl-1-[N alpha-(3-methyl-1,2,3,4-tetrahydro-8- quinolinesulphonyl)-L-arginyl]-2-piperidine carboxylic acid (MQPA) [Matzusaki, T., Sasaki, C., Okumura, C. & Umeyama (1989) J. Biochem. (Tokyo) 105, 949-952] were transferred in their trypsin-binding conformations to human alpha-thrombin [Bode, W., Mayr, I., Baumann, U., Huber, R., Stone, S. R. & Hofsteenge, J. (1989) EMBO J. 8. 3467 - 3475] and energy minimized. Both synthetic inhibitors fit perfectly into the much more restricted active site of thrombin. The accommodation of the S-aryl moieties in the 'aryl-binding site' and of the piperidine rings in the S2 subsite of thrombin are particularly favorable. The preference of thrombin for distinctly substituted piperidine derivatives and its generally higher (compared with trypsin) affinity for benzamidine and arginine-based inhibitors can be accounted for by these thrombin inhibitor models.
利用分辨率为0.18纳米的X射线数据测定了与Nα-(2-萘磺酰基-甘氨酰)-DL-对脒基苯丙氨酰哌啶（NAPAP）形成的胰蛋白酶复合物的X射线晶体结构，并进行了晶体学精修。NAPAP以相当紧密的形式结合到胰蛋白酶的活性位点：D-立体异构体的对脒基苯丙氨酸部分结合到特异性口袋中；甘氨酰基与Gly216形成氢键；萘基垂直于Trp215的吲哚部分；哌啶环紧密堆积在该萘基部分和His57之间；因此，NAPAP的羧基末端酰胺键的位置使其不易受到活性位点Ser195的作用。将NAPAP和(2R,4R)-4-甲基-1-[Nα-(3-甲基-1,2,3,4-四氢-8-喹啉磺酰基)-L-精氨酰]-2-哌啶羧酸（MQPA）[松崎，T.，佐佐木，C.，冈村，C. & 梅山（1989年）《生物化学杂志》（东京）105，949 - 952]以其与胰蛋白酶结合的构象转移到人α-凝血酶[博德，W.，迈尔，I.，鲍曼，U.，胡贝尔，R.，斯通，S. R. & 霍夫斯泰恩格，J.（1989年）《欧洲分子生物学组织杂志》8. 3467 - 3475]上并进行能量最小化。两种合成抑制剂都完美地契合到凝血酶更受限的活性位点中。凝血酶的“S-芳基结合位点”中S-芳基部分和S2亚位点中哌啶环的容纳情况特别有利。这些凝血酶抑制剂模型可以解释凝血酶对明显取代的哌啶衍生物的偏好及其（与胰蛋白酶相比）对苯甲脒和基于精氨酸的抑制剂通常更高的亲和力。
