3HPT | pdb_00003hpt

Crystal structure of human FxA in complex with (S)-2-cyano-1-(2-methylbenzofuran-5-yl)-3-(2-oxo-1-(2-oxo-2-(pyrrolidin-1-yl)ethyl)azepan-3-yl)guanidine

PDB DOI: https://doi.org/10.2210/pdb3HPT/pdb

Classification: HYDROLASE, BLOOD CLOTTING
Organism(s): Homo sapiens
Mutation(s): No

Deposited: 2009-06-04 Released: 2009-11-17
Deposition Author(s): Klei, H.E., Ghosh, K., Rushith, A., Kish, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.19 Å
R-Value Free:
0.239 (Depositor), 0.237 (DCC)
R-Value Work:
0.176 (Depositor)
R-Value Observed:
0.179 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Cyanoguanidine-based lactam derivatives as a novel class of orally bioavailable factor Xa inhibitors.

Shi, Y., Zhang, J., Shi, M., O'Connor, S.P., Bisaha, S.N., Li, C., Sitkoff, D., Pudzianowski, A.T., Chong, S., Klei, H.E., Kish, K., Yanchunas, J., Liu, E.C., Hartl, K.S., Seiler, S.M., Steinbacher, T.E., Schumacher, W.A., Atwal, K.S., Stein, P.D.

(2009) Bioorg Med Chem Lett 19: 4034-4041

PubMed: 19541481 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2009.06.014
Primary Citation Related Structures:
3HPT

PubMed Abstract:
The N,N'-disubstituted cyanoguanidine is an excellent bioisostere of the thiourea and ketene aminal functional groups. We report the design and synthesis of a novel class of cyanoguanidine-based lactam derivatives as potent and orally active FXa inhibitors. The SAR studies led to the discovery of compound 4 (BMS-269223, K(i)=6.5nM, EC(2xPT)=32muM) as a selective, orally bioavailable FXa inhibitor with an excellent in vitro liability profile, favorable pharmacokinetics and pharmacodynamics in animal models. The X-ray crystal structure of 4 bound in FXa is presented and key ligand-protein interactions are discussed.

Organizational Affiliation

Research and Development, Bristol-Myers Squibb Company, PO Box 5400, Princeton, NJ 08543-5400, USA. yan.shi@bms.com

Macromolecule Content

Total Structure Weight: 76.65 kDa
Atom Count: 5,683
Modeled Residue Count: 646
Deposited Residue Count: 664
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, C	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
PHAROS: 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, D	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
PHAROS: 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 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
YET Query on YET Download:Ideal Coordinates CCD File SDF format, chain Q [auth D] SDF format, chain G [auth B] MOL2 format, chain Q [auth D] MOL2 format, chain G [auth B] mmCIF format, chain Q [auth D] mmCIF format, chain G [auth B]	G [auth B], Q [auth D]	1-cyano-2-(2-methyl-1-benzofuran-5-yl)-3-[(3S)-2-oxo-1-(2-oxo-2-pyrrolidin-1-ylethyl)azepan-3-yl]guanidine C₂₃ H₂₈ N₆ O₃ BQUXAJWDRCSKFN-IBGZPJMESA-N		Interactions Focus chain G [auth B] Focus chain Q [auth D] Interactions & Density Focus chain G [auth B] Focus chain Q [auth D]
MES Query on MES Download:Ideal Coordinates CCD File SDF format, chain V [auth D] SDF format, chain K [auth B] MOL2 format, chain V [auth D] MOL2 format, chain K [auth B] mmCIF format, chain V [auth D] mmCIF format, chain K [auth B]	K [auth B], V [auth D]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Focus chain V [auth D] Interactions & Density Focus chain K [auth B] Focus chain V [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain U [auth D] SDF format, chain T [auth D] SDF format, chain J [auth B] SDF format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain U [auth D] MOL2 format, chain T [auth D] MOL2 format, chain J [auth B] MOL2 format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain U [auth D] mmCIF format, chain T [auth D] mmCIF format, chain J [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth A], J [auth B], T [auth D], U [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Focus chain T [auth D] Focus chain U [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Focus chain T [auth D] Focus chain U [auth D]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain Z [auth D] SDF format, chain O [auth B] MOL2 format, chain Z [auth D] MOL2 format, chain O [auth B] mmCIF format, chain Z [auth D] mmCIF format, chain O [auth B]	O [auth B], Z [auth D]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain O [auth B] Focus chain Z [auth D] Interactions & Density Focus chain O [auth B] Focus chain Z [auth D]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain Y [auth D] SDF format, chain X [auth D] SDF format, chain W [auth D] SDF format, chain P [auth B] SDF format, chain L [auth B] SDF format, chain AA [auth D] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain Y [auth D] MOL2 format, chain X [auth D] MOL2 format, chain W [auth D] MOL2 format, chain P [auth B] MOL2 format, chain L [auth B] MOL2 format, chain AA [auth D] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain Y [auth D] mmCIF format, chain X [auth D] mmCIF format, chain W [auth D] mmCIF format, chain P [auth B] mmCIF format, chain L [auth B] mmCIF format, chain AA [auth D]	AA [auth D] L [auth B] M [auth B] N [auth B] P [auth B] AA [auth D], L [auth B], M [auth B], N [auth B], P [auth B], W [auth D], X [auth D], Y [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain AA [auth D] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth B] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Interactions & Density Focus chain AA [auth D] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth B] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain R [auth D] SDF format, chain H [auth B] MOL2 format, chain R [auth D] MOL2 format, chain H [auth B] mmCIF format, chain R [auth D] mmCIF format, chain H [auth B]	H [auth B], R [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain R [auth D] Interactions & Density Focus chain H [auth B] Focus chain R [auth D]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain S [auth D] MOL2 format, chain I [auth B] MOL2 format, chain S [auth D] mmCIF format, chain I [auth B] mmCIF format, chain S [auth D]	I [auth B], S [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain S [auth D] Interactions & Density Focus chain I [auth B] Focus chain S [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.19 Å
R-Value Free: 0.239 (Depositor), 0.237 (DCC)
R-Value Work: 0.176 (Depositor)
R-Value Observed: 0.179 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.98	α = 90
b = 78.66	β = 102.49
c = 73.67	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-11-17

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-11-17
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2024-10-09
Changes: Data collection, Database references, Derived calculations, Structure summary