7KPB

Human TNF-alpha TNFR1 complex bound to conformationally selective antibody


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 

Starting Model: other
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

A conformation-selective monoclonal antibody against a small molecule-stabilised signalling-deficient form of TNF

Lightwood, D.J.Munro, R.J.Porter, J.McMillan, D.Carrington, B.Turner, A.Scott-Tucker, A.Hickford, E.S.Schmidt, A.Fox III, D.Maloney, A.Ceska, T.Bourne, T.O'Connell, J.Lawson, A.D.G.

(2021) Nat Commun 12: 583-583

  • DOI: https://doi.org/10.1038/s41467-020-20825-6
  • Primary Citation of Related Structures:  
    7KPA, 7KPB

  • PubMed Abstract: 

    We have recently described the development of a series of small-molecule inhibitors of human tumour necrosis factor (TNF) that stabilise an open, asymmetric, signalling-deficient form of the soluble TNF trimer. Here, we describe the generation, characterisation, and utility of a monoclonal antibody that selectively binds with high affinity to the asymmetric TNF trimer-small molecule complex. The antibody helps to define the molecular dynamics of the apo TNF trimer, reveals the mode of action and specificity of the small molecule inhibitors, acts as a chaperone in solving the human TNF-TNFR1 complex crystal structure, and facilitates the measurement of small molecule target occupancy in complex biological samples. We believe this work defines a role for monoclonal antibodies as tools to facilitate the discovery and development of small-molecule inhibitors of protein-protein interactions.


  • Organizational Affiliation

    UCB Pharma, 208 Bath Road, Slough, SL1 3WE, UK. Daniel.Lightwood@ucb.com.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tumor necrosis factor
A, B, C
158Homo sapiensMutation(s): 0 
Gene Names: TNFTNFATNFSF2
UniProt & NIH Common Fund Data Resources
Find proteins for P01375 (Homo sapiens)
Explore P01375 
Go to UniProtKB:  P01375
PHAROS:  P01375
GTEx:  ENSG00000232810 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01375
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Tumor necrosis factor receptor superfamily member 1AD [auth F],
E
144Homo sapiensMutation(s): 2 
Gene Names: TNFRSF1ATNFARTNFR1
UniProt & NIH Common Fund Data Resources
Find proteins for P19438 (Homo sapiens)
Explore P19438 
Go to UniProtKB:  P19438
PHAROS:  P19438
GTEx:  ENSG00000067182 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19438
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P19438-1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Fab1974 - Light ChainF [auth L]214Mus musculusMutation(s): 0 
Gene Names: mFab'nh CA_185_1974
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Fab1974 - Heavy ChainG [auth H]223Mus musculusMutation(s): 0 
Gene Names: mFab'nh CA_185_1974
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
D84 (Subject of Investigation/LOI)
Query on D84

Download Ideal Coordinates CCD File 
K [auth C]5-(1-{[2-(difluoromethoxy)phenyl]methyl}-2-{[3-(2-oxopyrrolidin-1-yl)phenoxy]methyl}-1H-benzimidazol-6-yl)pyridin-2(1H)-one
C31 H26 F2 N4 O4
DNTKSNFCNRDJAC-UHFFFAOYSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
O [auth E]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
H [auth A]
I [auth B]
J [auth B]
L [auth F]
M [auth F]
H [auth A],
I [auth B],
J [auth B],
L [auth F],
M [auth F],
N [auth F],
P [auth E],
Q [auth E],
R [auth L]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.51α = 90
b = 99.51β = 90
c = 311.35γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-13
    Type: Initial release
  • Version 1.1: 2021-02-03
    Changes: Database references
  • Version 1.2: 2022-06-29
    Changes: Database references, Structure summary
  • Version 1.3: 2023-05-24
    Changes: Database references, Structure summary
  • Version 1.4: 2024-04-03
    Changes: Data collection, Refinement description
  • Version 1.5: 2024-10-23
    Changes: Structure summary