9GOX | pdb_00009gox

Crystal structure of Fab B6-D9 in complex with CD38


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 
    0.208 (Depositor), 0.203 (DCC) 
  • R-Value Work: 
    0.174 (Depositor) 
  • R-Value Observed: 
    0.176 (Depositor) 

Starting Models: experimental
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Ligand Structure Quality Assessment 


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Literature

Biparatopic binding of ISB 1442 to CD38 in trans enables increased cell antibody density and increased avidity.

Loyau, J.Monney, T.Montefiori, M.Bokhovchuk, F.Streuli, J.Blackburn, M.Goepfert, A.Caro, L.N.Chakraborti, S.De Angelis, S.Grandclement, C.Blein, S.Mbow, M.L.Srivastava, A.Perro, M.Sammicheli, S.Zhukovsky, E.A.Dyson, M.Dreyfus, C.

(2025) MAbs 17: 2457471-2457471

  • DOI: https://doi.org/10.1080/19420862.2025.2457471
  • Primary Citation Related Structures: 
    9GOX, 9GOY

  • PubMed Abstract: 

    ISB 1442 is a bispecific biparatopic antibody in clinical development to treat hematological malignancies. It consists of two adjacent anti-CD38 arms targeting non-overlapping epitopes that preferentially drive binding to tumor cells and a low-affinity anti-CD47 arm to enable avidity-induced blocking of proximal CD47 receptors. We previously reported the pharmacology of ISB 1442, designed to reestablish synthetic immunity in CD38+ hematological malignancies. Here, we describe the discovery, optimization and characterization of the ISB 1442 antigen binding fragment (Fab) arms, their assembly to 2 + 1 format, and present the high-resolution co-crystal structures of the two anti-CD38 Fabs, in complex with CD38. This, with biophysical and functional assays, elucidated the underlying mechanism of action of ISB 1442. In solution phase, ISB 1442 forms a 2:2 complex with CD38 as determined by size-exclusion chromatography with multi-angle light scattering and electron microscopy. The predicted antibody-antigen stoichiometries at different CD38 surface densities were experimentally validated by surface plasmon resonance and cell binding assays. The specific design and structural features of ISB 1442 enable: 1) enhanced trans binding to adjacent CD38 molecules to increase Fc density at the cancer cell surface; 2) prevention of avid cis binding to monomeric CD38 to minimize blockade by soluble shed CD38; and 3) greater binding avidity, with a slower off-rate at high CD38 density, for increased specificity. The superior CD38 targeting of ISB 1442, at both high and low receptor densities, by its biparatopic design, will enhance proximal CD47 blockade and thus counteract a major tumor escape mechanism in multiple myeloma patients.


  • Organizational Affiliation
    • Ichnos Glenmark Innovation, New York, NY, USA.

Macromolecule Content 

  • Total Structure Weight: 80.01 kDa 
  • Atom Count: 6,331 
  • Modeled Residue Count: 686 
  • Deposited Residue Count: 702 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab B6-D9 heavy chainA [auth H]224Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab B6-D9 light chainB [auth L]214Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1C [auth A]264Homo sapiensMutation(s): 0 
Gene Names: CD38
EC: 3.2.2 (PDB Primary Data), 3.2.2.6 (PDB Primary Data), 2.4.99.20 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P28907 (Homo sapiens)
Explore P28907 
Go to UniProtKB:  P28907
PHAROS:  P28907
GTEx:  ENSG00000004468 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28907
Glycosylation
Glycosylation Sites: 3Go to GlyGen: P28907-1
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EPE

Query on EPE



Download:Ideal Coordinates CCD File
T [auth A]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
H [auth A],
I [auth A],
J [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
D [auth H],
K [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
N [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
E [auth H]
F [auth L]
G [auth L]
L [auth A]
M [auth A]
E [auth H],
F [auth L],
G [auth L],
L [auth A],
M [auth A],
O [auth A],
P [auth A],
R [auth A],
S [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
Q [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free:  0.208 (Depositor), 0.203 (DCC) 
  • R-Value Work:  0.174 (Depositor) 
  • R-Value Observed: 0.176 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 166.045α = 90
b = 166.045β = 90
c = 78.769γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
XDSdata reduction
autoPROCdata reduction
autoPROCdata scaling
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateSwitzerland--

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-12
    Type: Initial release