8CN9

Factor VII binding Fab of the bispecific antibody HMB-001 in complex with Factor VII


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.356 
  • R-Value Work: 0.303 
  • R-Value Observed: 0.305 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

A bispecific antibody approach for the potential prophylactic treatment of inherited bleeding disorders.

Gandhi, P.S.Zivkovic, M.Ostergaard, H.Bonde, A.C.Elm, T.Lovgreen, M.N.Schluckebier, G.Johansson, E.Olsen, O.H.Olsen, E.H.N.de Bus, I.A.Bloem, K.Alskar, O.Rea, C.J.Bjorn, S.E.Schutgens, R.E.Sorensen, B.Urbanus, R.T.Faber, J.H.

(2024) Nat Cardiovasc Res 3: 166-185

  • DOI: https://doi.org/10.1038/s44161-023-00418-4
  • Primary Citation of Related Structures:  
    8CHE, 8CN9

  • PubMed Abstract: 

    Inherited bleeding disorders such as Glanzmann thrombasthenia (GT) lack prophylactic treatment options. As a result, serious bleeding episodes are treated acutely with blood product transfusions or frequent, repeated intravenous administration of recombinant activated coagulation factor VII (rFVIIa). Here we describe HMB-001, a bispecific antibody designed to bind and accumulate endogenous FVIIa and deliver it to sites of vascular injury by targeting it to the TREM (triggering receptor expressed on myeloid cells)-like transcript-1 (TLT-1) receptor that is selectively expressed on activated platelets. In healthy nonhuman primates, HMB-001 prolonged the half-life of endogenous FVIIa, resulting in its accumulation. Mouse bleeding studies confirmed antibody-mediated potentiation of FVIIa hemostatic activity by TLT-1 targeting. In ex vivo models of GT, HMB-001 localized FVIIa on activated platelets and potentiated fibrin-dependent platelet aggregation. Taken together, these results indicate that HMB-001 has the potential to offer subcutaneous prophylactic treatment to prevent bleeds in people with GT and other inherited bleeding disorders, with a low-frequency dosing regimen.


  • Organizational Affiliation

    Hemab Therapeutics, Copenhagen, Denmark. [email protected].


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fab light chain
A, F, K, P
214Homo sapiensMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fab heavy chain
B, G, L, Q
220Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Coagulation factor VII
C, H, M, R
254Homo sapiensMutation(s): 0 
Gene Names: F7
EC: 3.4.21.21
UniProt & NIH Common Fund Data Resources
Find proteins for P08709 (Homo sapiens)
Explore P08709 
Go to UniProtKB:  P08709
PHAROS:  P08709
GTEx:  ENSG00000057593 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08709
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Coagulation factor VII
D, I, N, S
107Homo sapiensMutation(s): 0 
Gene Names: F7
EC: 3.4.21.21
UniProt & NIH Common Fund Data Resources
Find proteins for P08709 (Homo sapiens)
Explore P08709 
Go to UniProtKB:  P08709
PHAROS:  P08709
GTEx:  ENSG00000057593 
Entity Groups  
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UniProt GroupP08709
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Tissue factor
E, J, O, T
219Homo sapiensMutation(s): 0 
Gene Names: F3
UniProt & NIH Common Fund Data Resources
Find proteins for P13726 (Homo sapiens)
Explore P13726 
Go to UniProtKB:  P13726
PHAROS:  P13726
GTEx:  ENSG00000117525 
Entity Groups  
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UniProt GroupP13726
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BGC
Query on BGC

Download Ideal Coordinates CCD File 
AA [auth I],
HA [auth S],
W [auth D]
beta-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
CS
Query on CS

Download Ideal Coordinates CCD File 
EA [auth P]CESIUM ION
Cs
NCMHKCKGHRPLCM-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
BA [auth K]
CA [auth M]
DA [auth M]
FA [auth R]
GA [auth R]
BA [auth K],
CA [auth M],
DA [auth M],
FA [auth R],
GA [auth R],
U [auth A],
V [auth C],
X [auth F],
Y [auth H],
Z [auth H]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.356 
  • R-Value Work: 0.303 
  • R-Value Observed: 0.305 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.782α = 90
b = 100.794β = 101.22
c = 181.739γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data collection
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-27
    Type: Initial release
  • Version 1.1: 2024-09-11
    Changes: Database references
  • Version 1.2: 2024-11-20
    Changes: Structure summary