GeezerVison is showing www.rcsb.org — RCSB PDB - 3SW2: X-ray crystal structure of human FXA in complex with 6-chloro-N-((3S)-2-oxo-1-(2-oxo-2-((5S)-8-oxo-5,6-dihydro-1H-1,5-methanopyrido[1,2-a][1,5]diazocin-3(2H,4H,8H)-yl)ethyl)piperidin-3-yl)naphthalene-2-sulfonamide

3SW2 | pdb_00003sw2

X-ray crystal structure of human FXA in complex with 6-chloro-N-((3S)-2-oxo-1-(2-oxo-2-((5S)-8-oxo-5,6-dihydro-1H-1,5-methanopyrido[1,2-a][1,5]diazocin-3(2H,4H,8H)-yl)ethyl)piperidin-3-yl)naphthalene-2-sulfonamide

PDB DOI: https://doi.org/10.2210/pdb3SW2/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Homo sapiens
Mutation(s): No

Deposited: 2011-07-13 Released: 2011-11-16
Deposition Author(s): Klei, H.E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.42 Å
R-Value Free:
0.262 (Depositor), 0.255 (DCC)
R-Value Work:
0.193 (Depositor), 0.183 (DCC)
R-Value Observed:
0.199 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

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Arylsulfonamidopiperidone derivatives as a novel class of factor Xa inhibitors.

Shi, Y., O'Connor, S.P., Sitkoff, D., Zhang, J., Shi, M., Bisaha, S.N., Wang, Y., Li, C., Ruan, Z., Michael Lawrence, R., Klei, H.E., Kish, K., Liu, E.C., Seiler, S.M., Schweizer, L., Steinbacher, T.E., Schumacher, W.A., Robl, J.A., Macor, J.E., Atwal, K.S., Stein, P.D.

(2011) Bioorg Med Chem Lett 21: 7516-7521

PubMed: 22041058 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2011.06.098
Primary Citation Related Structures:
3SW2

PubMed Abstract:
The design, synthesis and SAR of a novel class of valerolactam-based arylsulfonamides as potent and selective FXa inhibitors is reported. The arylsulfonamide-valerolactam scaffold was derived based on the proposed bioisosterism to the arylcyanoguanidine-caprolactam core in known FXa inhibitors. The SAR study led to compound 46 as the most potent FXa inhibitor in this series, with an IC(50) of 7 nM and EC(2×PT) of 1.7 μM. The X-ray structure of compound 40 bound to FXa shows that the sulfonamide-valerolactam scaffold anchors the aryl group in the S1 and the novel acylcytisine pharmacophore in the S4 pockets.

Organizational Affiliation

Research and Development, Bristol-Myers Squibb Company, PO Box 5400, Princeton, NJ 08543-5400, USA. Michael

Asymmetric Unit

Explore in 3D: Structure | Sequence Annotations | Electron Density | Validation Report | Ligand Interaction (FI1)

Biological Assembly 1

Explore in 3D: Structure | Sequence Annotations | Electron Density | Validation Report | Ligand Interaction (FI1)

Global Symmetry: Asymmetric - C1
Global Stoichiometry: Hetero 2-mer - A1B1

Find Similar Assemblies

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

Total Structure Weight: 37.81 kDa
Atom Count: 2,283
Modeled Residue Count: 289
Deposited Residue Count: 332
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor X	A	94	Homo sapiens	Mutation(s): 0 EC: 3.4.21.6
UniProt & NIH Common Fund Data Resources
Find proteins for P00742 (Homo sapiens) Explore P00742 Go to UniProtKB: P00742
GTEx: ENSG00000126218
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00742
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor X	B	238	Homo sapiens	Mutation(s): 0 EC: 3.4.21.6
UniProt & NIH Common Fund Data Resources
Find proteins for P00742 (Homo sapiens) Explore P00742 Go to UniProtKB: P00742
GTEx: ENSG00000126218
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00742
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FI1 Query on FI1 Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	6-chloro-N-((3S)-2-oxo-1-(2-oxo-2-((5S)-8-oxo-5,6-dihydro-1H-1,5-methanopyrido[1,2-a][1,5]diazocin-3(2H,4H,8H)-yl)ethyl)piperidin-3-yl)naphthalene-2-sulfonamide C₂₈ H₂₉ Cl N₄ O₅ S FLGSVBQCPOVGER-VNZMSGEBSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
FI1	BindingDB: 3SW2	Ki: 4.71 (nM) from 1 assay(s)
FI1	BindingDB: 3SW2	IC50: 13 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.42 Å
R-Value Free: 0.262 (Depositor), 0.255 (DCC)
R-Value Work: 0.193 (Depositor), 0.183 (DCC)
R-Value Observed: 0.199 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.018	α = 90
b = 72.515	β = 90
c = 77.956	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
AMoRE	phasing
PHENIX	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-11-16

Deposition Author(s):

Klei, H.E.

Revision History (Full details and data files)

Version 1.0: 2011-11-16
Type: Initial release
Version 1.1: 2011-12-07
Changes: Database references
Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-10-30
Changes: Structure summary

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