5EGM | pdb_00005egm

Development of a novel tricyclic class of potent and selective FIXa inhibitors


Experimental Data Snapshot

  • Method:&nbspX-RAY DIFFRACTION
  • Resolution:&nbsp1.84 Å
  • R-Value Free:&nbsp
    0.171 (Depositor), 0.154 (DCC)&nbsp
  • R-Value Work:&nbsp
    0.148 (Depositor)&nbsp
  • R-Value Observed:&nbsp
    0.149&nbsp(Depositor)&nbsp

Starting Model: experimental
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Ligand Structure Quality Assessment&nbsp


This is version 1.3 of the entry. See complete&nbsphistory.&nbsp

Literature

Development of a novel tricyclic class of potent and selective FIXa inhibitors.

Meng, D.,&nbspAndre, P.,&nbspBateman, T.J.,&nbspBerger, R.,&nbspChen, Y.H.,&nbspDesai, K.,&nbspDewnani, S.,&nbspEllsworth, K.,&nbspFeng, D.,&nbspGeissler, W.M.,&nbspGuo, L.,&nbspHruza, A.,&nbspJian, T.,&nbspLi, H.,&nbspMetzger, J.,&nbspParker, D.L.,&nbspReichert, P.,&nbspSherer, E.C.,&nbspSmith, C.J.,&nbspSonatore, L.M.,&nbspTschirret-Guth, R.,&nbspWu, J.,&nbspXu, J.,&nbspZhang, T.,&nbspCampeau, L.C.,&nbspOrr, R.,&nbspPoirier, M.,&nbspMcCabe-Dunn, J.,&nbspAraki, K.,&nbspNishimura, T.,&nbspSakurada, I.,&nbspHirabayashi, T.,&nbspWood, H.B.

(2015) Bioorg Med Chem Lett&nbsp25: 5437-5443

  • DOI:&nbsphttps://doi.org/10.1016/j.bmcl.2015.07.078
  • Primary Citation Related Structures:&nbsp
    5EGM

  • PubMed Abstract:&nbsp

    Using structure based drug design, a novel class of potent coagulation factor IXa (FIXa) inhibitors was designed and synthesized. High selectivity over FXa inhibition was achieved. Selected compounds were evaluated in rat IV/PO pharmacokinetic (PK) studies and demonstrated desirable oral PK profiles. Finally, the pharmacodynamics (PD) of this class of molecules were evaluated in thrombin generation assay (TGA) in Corn Trypsin Inhibitor (CTI) citrated human plasma and demonstrated characteristics of a FIXa inhibitor.


  • Organizational Affiliation:&nbsp
    • Department of Discovery Chemistry, Merck Research Laboratories, Merck & Co., Inc., PO Box 2000, Rahway, NJ 07065, USA. Electronic address: [email protected].

Macromolecule Content&nbsp

  • Total Structure Weight: 33.73 kDa&nbsp
  • Atom Count: 2,565&nbsp
  • Modeled Residue Count: 289&nbsp
  • Deposited Residue Count: 297&nbsp
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Coagulation factor IX235Homo sapiensMutation(s): 1&nbsp
Gene Names:&nbspF9
EC:&nbsp3.4.21.22
UniProt & NIH Common Fund Data Resources
Find proteins for&nbspP00740&nbsp(Homo sapiens)
Explore&nbspP00740&nbsp
Go to UniProtKB: &nbspP00740
PHAROS: &nbspP00740
GTEx: &nbspENSG00000101981&nbsp
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00740
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Coagulation factor IX62Homo sapiensMutation(s): 0&nbsp
Gene Names:&nbspF9
EC:&nbsp3.4.21.22
UniProt & NIH Common Fund Data Resources
Find proteins for&nbspP00740&nbsp(Homo sapiens)
Explore&nbspP00740&nbsp
Go to UniProtKB: &nbspP00740
PHAROS: &nbspP00740
GTEx: &nbspENSG00000101981&nbsp
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00740
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands&nbsp3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
5NY

Query on 5NY



Download:Ideal Coordinates CCD File
E [auth A]2-chloranyl-~{N}-[(7~{S})-2-methyl-7-phenyl-10-(1~{H}-1,2,3,4-tetrazol-5-yl)-8,9-dihydro-6~{H}-pyrido[1,2-a]indol-7-yl]-4-(1,2,4-triazol-4-yl)benzamide
C29 H24 Cl N9 O
TUCDMISJVGVBLL-GDLZYMKVSA-N
NHE

Query on NHE



Download:Ideal Coordinates CCD File
D [auth A]2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
C8 H17 N O3 S
MKWKNSIESPFAQN-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
C [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method:&nbspX-RAY DIFFRACTION
  • Resolution:&nbsp1.84 Å
  • R-Value Free:&nbsp 0.171 (Depositor), 0.154 (DCC)&nbsp
  • R-Value Work:&nbsp 0.148 (Depositor)&nbsp
  • R-Value Observed:&nbsp0.149&nbsp(Depositor)&nbsp
Space Group:&nbspH 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.298α = 90
b = 99.298β = 90
c = 94.685γ = 120
Software Package:
Software NamePurpose
autoPROCdata scaling
XDSdata reduction
SCALAdata scaling
MOLREPphasing
BUSTERrefinement

Structure Validation

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Ligand Structure Quality Assessment&nbsp


Entry History&nbsp

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-18
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Derived calculations, Refinement description
  • Version 1.2: 2023-09-27
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-11-20
    Changes: Structure summary