4DTG

Hemostatic effect of a monoclonal antibody mAb 2021 blocking the interaction between FXa and TFPI in a rabbit hemophilia model

PDB DOI: https://doi.org/10.2210/pdb4DTG/pdb

Classification: BLOOD CLOTTING INHIBITOR/IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Homo sapiens, Escherichia coli
Mutation(s): No

Deposited: 2012-02-21 Released: 2012-06-13
Deposition Author(s): Svensson, L.A., Breinholt, J., Krogh, B.O., Hilden, I.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.236
R-Value Work: 0.196
R-Value Observed: 0.198

wwPDB Validation 3D Report Full Report

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

Literature

Hemostatic effect of a monoclonal antibody mAb 2021 blocking the interaction between FXa and TFPI in a rabbit hemophilia model.

Hilden, I., Lauritzen, B., Sorensen, B.B., Clausen, J.T., Jespersgaard, C., Krogh, B.O., Bowler, A.N., Breinholt, J., Gruhler, A., Svensson, L.A., Petersen, H.H., Petersen, L.C., Balling, K.W., Hansen, L., Hermit, M.B., Egebjerg, T., Friederichsen, B., Ezban, M., Bjorn, S.E.

(2012) Blood 119: 5871-5878

PubMed: 22563084 Search on PubMed
DOI: https://doi.org/10.1182/blood-2012-01-401620
Primary Citation of Related Structures:
4DTG

PubMed Abstract:
Hemophilia is treated by IV replacement therapy with Factor VIII (FVIII) or Factor IX (FIX), either on demand to resolve bleeding, or as prophylaxis. Improved treatment may be provided by drugs designed for subcutaneous and less frequent administration with a reduced risk of inhibitor formation. Tissue factor pathway inhibitor (TFPI) down-regulates the initiation of coagulation by inhibition of Factor VIIa (FVIIa)/tissue factor/Factor Xa (FVIIa/TF/FXa). Blockage of TFPI inhibition may facilitate thrombin generation in a hemophilic setting. A high-affinity (K(D) = 25pM) mAb, mAb 2021, against TFPI was investigated. Binding of mAb 2021 to TFPI effectively prevented inhibition of FVIIa/TF/FXa and improved clot formation in hemophilia blood and plasma. The binding epitope on the Kunitz-type protease inhibitor domain 2 of TFPI was mapped by crystallography, and showed an extensive overlap with the FXa contact region highlighting a structural basis for its mechanism of action. In a rabbit hemophilia model, an intravenous or subcutaneous dose significantly reduced cuticle bleeding. mAb 2021 showed an effect comparable with that of rFVIIa. Cuticle bleeding in the model was reduced for at least 7 days by a single intravenous dose of mAb 2021. This study suggests that neutralization of TFPI by mAb 2021 may constitute a novel treatment option in hemophilia.

Organizational Affiliation

Biopharmaceuticals Research Unit, Novo Nordisk, Maaloev, Denmark. IDAH@novonordisk.com

Macromolecule Content

Total Structure Weight: 57.1 kDa
Atom Count: 4,431
Modelled Residue Count: 500
Deposited Residue Count: 507
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Humanized recombinant FAB fragment, FAB 2021, of a murine antibody, light chain	A [auth L]	219	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Humanized recombinant FAB fragment, FAB 2021, of a murine antibody, heavy chain	B [auth H]	222	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Tissue factor pathway inhibitor	C [auth K]	66	Homo sapiens	Mutation(s): 0 Gene Names: LACI, TFPI, TFPI (AMINO ACIDS 119-178), TFPI1
UniProt & NIH Common Fund Data Resources
Find proteins for P10646 (Homo sapiens) Explore P10646 Go to UniProtKB: P10646
PHAROS: P10646 GTEx: ENSG00000003436
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P10646
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain K [auth H] MOL2 format, chain K [auth H]	K [auth H]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain K [auth H] Interactions & Density Focus chain K [auth H]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain L [auth H] SDF format, chain M [auth H] SDF format, chain N [auth H] MOL2 format, chain L [auth H] MOL2 format, chain M [auth H] MOL2 format, chain N [auth H]	L [auth H], M [auth H], N [auth H]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain L [auth H] Focus chain M [auth H] Focus chain N [auth H] Interactions & Density Focus chain L [auth H] Focus chain M [auth H] Focus chain N [auth H]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth L] SDF format, chain E [auth L] SDF format, chain F [auth L] SDF format, chain G [auth L] SDF format, chain H [auth L] SDF format, chain I [auth L] SDF format, chain J [auth L] SDF format, chain O [auth H] SDF format, chain P [auth H] SDF format, chain Q [auth H] MOL2 format, chain D [auth L] MOL2 format, chain E [auth L] MOL2 format, chain F [auth L] MOL2 format, chain G [auth L] MOL2 format, chain H [auth L] MOL2 format, chain I [auth L] MOL2 format, chain J [auth L] MOL2 format, chain O [auth H] MOL2 format, chain P [auth H] MOL2 format, chain Q [auth H]	D [auth L] E [auth L] F [auth L] G [auth L] H [auth L] D [auth L], E [auth L], F [auth L], G [auth L], H [auth L], I [auth L], J [auth L], O [auth H], P [auth H], Q [auth H]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth L] Focus chain E [auth L] Focus chain F [auth L] Focus chain G [auth L] Focus chain H [auth L] Focus chain I [auth L] Focus chain J [auth L] Focus chain O [auth H] Focus chain P [auth H] Focus chain Q [auth H] Interactions & Density Focus chain D [auth L] Focus chain E [auth L] Focus chain F [auth L] Focus chain G [auth L] Focus chain H [auth L] Focus chain I [auth L] Focus chain J [auth L] Focus chain O [auth H] Focus chain P [auth H] Focus chain Q [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.236
R-Value Work: 0.196
R-Value Observed: 0.198
Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.01	α = 90
b = 125.64	β = 90
c = 202.34	γ = 90

Software Package:

Software Name	Purpose
MxCuBE	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-06-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-06-13
Type: Initial release
Version 1.1: 2012-07-25
Changes: Database references
Version 1.2: 2018-03-07
Changes: Data collection
Version 1.3: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description