Biological Assembly 1  

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 23886.00 
• Atom Count: 1667 
• Residue Count: 223 
• Unique protein chains: 1

1PPC

GEOMETRY OF BINDING OF THE BENZAMIDINE-AND ARGININE-BASED INHIBITORS N-ALPHA-(2-NAPHTHYL-SULPHONYL-GLYCYL)-DL-P-AMIDINOPHENYLALANYL-PIPERIDINE (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

• DOI: 10.2210/pdb1PPC/pdb

• Classification: HYDROLASE/hydrolase inhibitor
• Organism(s): Bos taurus


• Deposited: 1991-10-24 Released: 1994-01-31 
• Deposition Author(s): Bode, W., Turk, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Work: 0.181 

Literature

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-tetrahydr 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.

Bode, W., Turk, D., Sturzebecher, J.

(1990) Eur.J.Biochem. 193: 175-182

• PubMed: 2226434 
• Also Cited By: 1DWE, 1DWD, 1DWC, 1DWB


• PubMed 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.

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Related Citations: 

• Geometry of Binding of the Nalpha-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
  Turk, D.,Stuerzebecher, J.,Bode, W.
  (1991) FEBS Lett. 287: 133
• The Refined 1.9 Angstroms Crystal Structure of Human Alpha-Thrombin: Interaction with D-Phe-Pro-Arg Chloromethylketone and Significance of the Tyr-Pro-Pro-Trp Insertion Segment
  Bode, W.,Mayr, I.,Baumann, U.,Huber, R.,Stone, S.R.,Hofsteenge, J.
  (1989) Embo J. 8: 3467
• Crystal Structure of Bovine Beta-Trypsin at 1.5 Angstroms Resolution in a Crystal Form with Low Molecular Packing Density. Active Site Geometry, Ion Pairs and Solvent Structure
  Bartunik, H.D.,Summers, L.J.,Bartsch, H.H.
  (1989) J.Mol.Biol. 210: 813
• The Refined Crystal Structure of Bovine Beta-Trypsin at 1.8 Angstroms Resolution. Crystallographic Refinement, Calcium Binding Site, Benzamidine Binding Site and Active Site at Ph 7.0
  Bode, W.,Schwager, P.
  (1975) J.Mol.Biol. 98: 693
• Refined 2.3 Angstroms 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
  Brandstetter, H.,Turk, D.,Hoeffken, H.W.,Grosse, D.,Stuerzebecher, J.,Martin, P.D.,Edwards, B.F.,Bode, W.
  (1992) J.Mol.Biol. 226: 1085
• The Refined 1.9 Angstroms 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
  Bode, W.,Turk, D.,Karshikov, A.
  (1992) Protein Sci. 1: 426




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Organizational Affiliation: 

Max-Planck-Institut für Biochemie, Martinsried, Federal Republic of Germany.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
TRYPSIN	E	223	Bos taurus	Mutation(s): 0  EC: 3.4.21.4
Find proteins for P00760 (Bos taurus) Go to UniProtKB:  P00760

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
MID	E	1-[N-(naphthalen-2-ylsulfonyl)glycyl-4-carbamimidoyl-D-phenylalanyl]piperidine NAPAP C27 H31 N5 O4 S XXTWZTPVNIYSJZ-XMMPIXPASA-N
CA	E	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Biologically Interesting Molecules 1 Unique
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000451 (MID)	E	N(alpha)-(2-naphthylsulfonylglycyl)-4-amidinophenylalanine piperidide	Peptide-like / Inhibitor		--

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
MID	Ki: 325 - 690 nM (100) BINDINGDB
MID	Ki: 690 nM BINDINGMOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Work: 0.181 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 63.510	α = 90.00
b = 69.190	β = 90.00
c = 63.810	γ = 90.00

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1991-10-24 
• Released Date: 1994-01-31 
• Deposition Author(s): Bode, W., Turk, D.

Revision History 

• Version 1.0: 1994-01-31
  Type: Initial release
• Version 1.1: 2008-05-22
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.3: 2012-12-12
  Type: Other