PDBsum entry 1ppc

Hydrolase/hydrolase inhibitor

PDB id: 1ppc

Contents

Protein chain

223 a.a. *

Ligands

MID

Metals

_CA

Waters ×147

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Geometry of binding of the benzamidine- And arginine-Based inhibitors n alpha-(2-Naphthyl-Sulphonyl-Glycyl)-Dl-P-Amidinophenylalanyl-Pipe ridine (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) to human alpha-Thrombin. X-Ray crystallographic determination of the napap-Trypsin complex and modeling of napap-Thrombin and mqpa-Thrombin.

Authors

W.Bode, D.Turk, J.Stürzebecher.

Ref.

Eur J Biochem, 1990, 193, 175-182.

PubMed id

2226434

Abstract

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.

Secondary reference #1

Title

Refined 2.3 a X-Ray crystal structure of bovine thrombin complexes formed with the benzamidine and arginine-Based thrombin inhibitors napap, 4-Tapap and mqpa. A starting point for improving antithrombotics.

Authors

H.Brandstetter, D.Turk, H.W.Hoeffken, D.Grosse, J.Stürzebecher, P.D.Martin, B.F.Edwards, W.Bode.

Ref.

J Mol Biol, 1992, 226, 1085-1099. [DOI no: 10.1016/0022-2836(92)91054-S]

PubMed id

1518046

Figure 1.
Figure 1. Chemical ormulas of NAPAP (with residues XasIl. GlypI2, Papal3 and Pipn14): (~cr-(2-napthyl-s~Ilphotl~l-

Figure 4.
Figure 4. ctive site region f the complex formed between NAPAP (thick lines) and bovine thrombin (thin lines) superimposed with the final 2F,,, -Fcslf electron denity. The view is (similar to Figs 2 and 3) towards the thrombin surface; the active site residues are o the ight, the specificity pocket is in the back. Contou surface is at @9a.

The above figures are reproduced from the cited reference with permission from Elsevier

Secondary reference #2

Title

The refined 1.9-A X-Ray crystal structure of d-Phe-Pro-Arg chloromethylketone-Inhibited human alpha-Thrombin: structure analysis, Overall structure, Electrostatic properties, Detailed active-Site geometry, And structure-Function relationships.

Authors

W.Bode, D.Turk, A.Karshikov.

Ref.

Protein Sci, 1992, 1, 426-471. [DOI no: 10.1002/pro.5560010402]

PubMed id

1304349

Figure 3.
Fig. 3. Tosyl-m-amidinophenylalanyl-piperidine (thickconnections), NAPAP (mediumconnections),and MQPA (thincon- nections)boundtotheactivesite of humana-thrombindisplayedtogetherwiththeConnollysurface f thrombin(Turk et al., 1991). The naphthyl/toluene/chinolyl groups of theinhibitorsinteractwiththearyl-bindingsiteofthrombin;thesidechains ofthe m- and thep-amidinophenylalanyl residues andofthe arginylresidueenterthespecificitypocketfrom slightly differing sites; the S2 subsiteofthrombin is occupiedtodifferentextentsbythe(partiallysubstituted)piperidinemoieties.The viewis similartothestandard view of Figure .

Figure 30.
Fig. 30. Luzzatiplot f thefinalthrombinmodelafterX-PLOR refinement.

The above figures are reproduced from the cited reference with permission from the Protein Society

Secondary reference #3

Title

Geometry of binding of the n alpha-Tosylated piperidides of m-Amidino-, P-Amidino- And p-Guanidino phenylalanine to thrombin and trypsin. X-Ray crystal structures of their trypsin complexes and modeling of their thrombin complexes.

Authors

D.Turk, J.Stürzebecher, W.Bode.

Ref.

FEBS Lett, 1991, 287, 133-138. [DOI no: 10.1016/0014-5793(91)80033-Y]

PubMed id

1879520

Secondary reference #4

Title

The refined 1.9 a crystal structure of human alpha-Thrombin: interaction with d-Phe-Pro-Arg chloromethylketone and significance of the tyr-Pro-Pro-Trp insertion segment.

Authors

W.Bode, I.Mayr, U.Baumann, R.Huber, S.R.Stone, J.Hofsteenge.

Ref.

Embo J, 1989, 8, 3467-3475.

PubMed id

2583108

Secondary reference #5

Title

Crystal structure of bovine beta-Trypsin at 1.5 a resolution in a crystal form with low molecular packing density. Active site geometry, Ion pairs and solvent structure.

Authors

H.D.Bartunik, L.J.Summers, H.H.Bartsch.

Ref.

J Mol Biol, 1989, 210, 813-828.

PubMed id

2614845

Secondary reference #6

Title

The refined crystal structure of bovine beta-Trypsin at 1.8 a resolution. Ii. Crystallographic refinement, Calcium binding site, Benzamidine binding site and active site at ph 7.0.

Authors

W.Bode, P.Schwager.

Ref.

J Mol Biol, 1975, 98, 693-717. [DOI no: 10.1016/S0022-2836(75)80005-2]

PubMed id

512

Figure 4.
FiG. 4. Stereo pair of the calcium-bindng loop including the calcium ion and internal water molecules.

Figure 7.
Fro. 7. Stereo pair of the region aroun the salt bridge between the benzamidine and Asp189 in benzamidine-inhibited trpsin (a) and side chain of LyslS(I) an Asp189 in he trysin- inhibitor complex (b), both in complex orientation.

The above figures are reproduced from the cited reference with permission from Elsevier