The X-ray crystal structure of thrombin in complex with N alpha-2-naphthylsulfonyl-L-3-amidino-phenylalanyl-4-methylpiperidide: the beneficial effect of filling out an empty cavity.
The 2.5 Angstrum structure of bovine epsilon-thrombin in complex with N alpha-2-naphthyl-sulfonyl-L-3-amidinophenylalanyl-4-methylpiper idide (L-NAPAMP) was solved and crystallographically refined to an R-value of 0.19. The L-NAPAMP moiety is completely and unambiguosly defined in the electron density. NAPAMP binds almost identical to the related 4-methyl deficient 3-amidino-phenylalanyl derivative TAPAP. The overall binding geometry appears dominated by the fixation of the 3-amidinophenyl ring in thrombin's S1-pocket and the hydrogen bonds to Gly 216, irrespective of the presence or absence of a substituent in the 4-position of the piperidine ring. The additional 4-methyl group gives rise to a 17-fold better binding. The more complete spatial occupancy of the hydrophobic S2-cavity therefore accounts for a decrease in free energy of binding of 15 kcal/mol, a value comparable with that anticipated for filling up a stable empty cavity of similar size by a methyl group.
Bergner
A
A
Max-Planck-Institut für Biochemie, München, Germany.
Bauer
M
M
Brandstetter
H
H
Stürzebecher
J
J
Bode
W
W
D000409:Alanine / Q000031:analogs & derivatives* / Q000737:chemistry / Q000378:metabolism; D000991:Antithrombins / Q000737:chemistry* / Q000378:metabolism / Q000494:pharmacology; D001665:Binding Sites; D003196:Computer Graphics; D018360:Crystallography, X-Ray; D004151:Dipeptides / Q000737:chemistry / Q000494:pharmacology; D008958:Models, Molecular; D010880:Piperidines / Q000737:chemistry* / Q000378:metabolism / Q000494:pharmacology; D011485:Protein Binding; D015842:Serine Proteinase Inhibitors / Q000737:chemistry* / Q000378:metabolism / Q000494:pharmacology; D013917:Thrombin / Q000037:antagonists & inhibitors* / Q000737:chemistry* / Q000378:metabolism
D000991:Antithrombins; D004151:Dipeptides; D010880:Piperidines; D015842:Serine Proteinase Inhibitors; C097938:1-(3-(3-(aminoiminomethyl)phenyl)-2-((2-naphthalenylsulfonyl)amino)-1-oxopropyl)-4-methylpiperidine; C035199:N(alpha)-tosyl-(3-amidinophenyl)alanine piperidide; C038708:N(alpha)-(2-naphthylsulfonylglycyl)-4-amidinophenylalanine piperidide; D013917:Thrombin; D000409:Alanine