5MU8 | pdb_00005mu8

HUMAN TNF-ALPHA IN COMPLEX WITH JNJ525

PDB DOI: https://doi.org/10.2210/pdb5MU8/pdb

Classification: CYTOKINE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-01-12 Released: 2017-03-29
Deposition Author(s): Blevitt, J.M., Hack, M.D., Herman, K.L., Jackson, P.F., Krawczuk, P.J., Lebsack, A.D., Liu, A.X., Mirzadegan, T., Nelen, M.I., Patrick, A.P., Steinbacher, S., Milla, M.E., Lumb, K.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.300 (Depositor), 0.304 (DCC)
R-Value Work:
0.211 (Depositor), 0.213 (DCC)
R-Value Observed:
0.211 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Structural Basis of Small-Molecule Aggregate Induced Inhibition of a Protein-Protein Interaction.

Blevitt, J.M., Hack, M.D., Herman, K.L., Jackson, P.F., Krawczuk, P.J., Lebsack, A.D., Liu, A.X., Mirzadegan, T., Nelen, M.I., Patrick, A.N., Steinbacher, S., Milla, M.E., Lumb, K.J.

(2017) J Med Chem 60: 3511-3517

PubMed: 28300404 Search on PubMed
DOI: https://doi.org/10.1021/acs.jmedchem.6b01836
Primary Citation Related Structures:
5MU8

PubMed Abstract:
A prevalent observation in high-throughput screening and drug discovery programs is the inhibition of protein function by small-molecule compound aggregation. Here, we present the X-ray structural description of aggregation-based inhibition of a protein-protein interaction involving tumor necrosis factor α (TNFα). An ordered conglomerate of an aggregating small-molecule inhibitor (JNJ525) induces a quaternary structure switch of TNFα that inhibits the protein-protein interaction between TNFα and TNFα receptors. SPD-304 may employ a similar mechanism of inhibition.

Organizational Affiliation

Emerging Science & Innovation, Discovery Sciences, Janssen R&D LLC , La Jolla, California 92121, United States.

Macromolecule Content

Total Structure Weight: 867.17 kDa
Atom Count: 56,305
Modeled Residue Count: 6,955
Deposited Residue Count: 7,632
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tumor necrosis factor	A AA [auth b] B BA [auth c] C A, AA [auth b], B, BA [auth c], C, CA [auth d], D, DA [auth e], E [auth F], EA [auth f], F [auth G], FA [auth g], G [auth H], GA [auth h], H [auth I], HA [auth i], I [auth J], IA [auth j], J [auth K], JA [auth k], K [auth L], KA [auth l], L [auth M], LA [auth m], M [auth N], MA [auth n], N [auth O], NA [auth o], O [auth P], OA [auth p], P [auth Q], PA [auth q], Q [auth R], QA [auth r], R [auth S], RA [auth s], S [auth T], SA [auth t], T [auth U], TA [auth u], U [auth V], UA [auth v], V [auth W], VA [auth w], W [auth X], X [auth Y], Y [auth Z], Z [auth a]	159	Homo sapiens	Mutation(s): 0 Gene Names: TNF, TNFA, TNFSF2
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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01375
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
JNI Query on JNI Download:Ideal Coordinates CCD File SDF format, chain AC [auth h] SDF format, chain CB [auth F] SDF format, chain DB [auth H] SDF format, chain DC [auth j] SDF format, chain EB [auth H] SDF format, chain EC [auth l] SDF format, chain FB [auth J] SDF format, chain FC [auth n] SDF format, chain GB [auth J] SDF format, chain GC [auth n] SDF format, chain HB [auth L] SDF format, chain HC [auth o] SDF format, chain IB [auth M] SDF format, chain IC [auth p] SDF format, chain JB [auth N] SDF format, chain JC [auth p] SDF format, chain KB [auth P] SDF format, chain LB [auth P] SDF format, chain MB [auth Q] SDF format, chain MC [auth t] SDF format, chain NB [auth R] SDF format, chain NC [auth t] SDF format, chain OB [auth U] SDF format, chain PB [auth V] SDF format, chain TB [auth Z] SDF format, chain VB [auth b] SDF format, chain WA [auth A] SDF format, chain XB [auth d] SDF format, chain YA [auth C] SDF format, chain ZB [auth f] SDF format, chain ZA [auth C] SDF format, chain YB [auth f] SDF format, chain XA [auth A] SDF format, chain WB [auth b] SDF format, chain UB [auth Z] SDF format, chain SB [auth X] SDF format, chain RB [auth X] SDF format, chain QB [auth V] SDF format, chain PC [auth v] SDF format, chain OC [auth v] SDF format, chain LC [auth r] SDF format, chain KC [auth r] SDF format, chain CC [auth j] SDF format, chain BC [auth h] SDF format, chain BB [auth F] SDF format, chain AB [auth D] MOL2 format, chain AC [auth h] MOL2 format, chain CB [auth F] MOL2 format, chain DB [auth H] MOL2 format, chain DC [auth j] MOL2 format, chain EB [auth H] MOL2 format, chain EC [auth l] MOL2 format, chain FB [auth J] MOL2 format, chain FC [auth n] MOL2 format, chain GB [auth J] MOL2 format, chain GC [auth n] MOL2 format, chain HB [auth L] MOL2 format, chain HC [auth o] MOL2 format, chain IB [auth M] MOL2 format, chain IC [auth p] MOL2 format, chain JB [auth N] MOL2 format, chain JC [auth p] MOL2 format, chain KB [auth P] MOL2 format, chain LB [auth P] MOL2 format, chain MB [auth Q] MOL2 format, chain MC [auth t] MOL2 format, chain NB [auth R] MOL2 format, chain NC [auth t] MOL2 format, chain OB [auth U] MOL2 format, chain PB [auth V] MOL2 format, chain TB [auth Z] MOL2 format, chain VB [auth b] MOL2 format, chain WA [auth A] MOL2 format, chain XB [auth d] MOL2 format, chain YA [auth C] MOL2 format, chain ZB [auth f] MOL2 format, chain ZA [auth C] MOL2 format, chain YB [auth f] MOL2 format, chain XA [auth A] MOL2 format, chain WB [auth b] MOL2 format, chain UB [auth Z] MOL2 format, chain SB [auth X] MOL2 format, chain RB [auth X] MOL2 format, chain QB [auth V] MOL2 format, chain PC [auth v] MOL2 format, chain OC [auth v] MOL2 format, chain LC [auth r] MOL2 format, chain KC [auth r] MOL2 format, chain CC [auth j] MOL2 format, chain BC [auth h] MOL2 format, chain BB [auth F] MOL2 format, chain AB [auth D] mmCIF format, chain AC [auth h] mmCIF format, chain CB [auth F] mmCIF format, chain DB [auth H] mmCIF format, chain DC [auth j] mmCIF format, chain EB [auth H] mmCIF format, chain EC [auth l] mmCIF format, chain FB [auth J] mmCIF format, chain FC [auth n] mmCIF format, chain GB [auth J] mmCIF format, chain GC [auth n] mmCIF format, chain HB [auth L] mmCIF format, chain HC [auth o] mmCIF format, chain IB [auth M] mmCIF format, chain IC [auth p] mmCIF format, chain JB [auth N] mmCIF format, chain JC [auth p] mmCIF format, chain KB [auth P] mmCIF format, chain LB [auth P] mmCIF format, chain MB [auth Q] mmCIF format, chain MC [auth t] mmCIF format, chain NB [auth R] mmCIF format, chain NC [auth t] mmCIF format, chain OB [auth U] mmCIF format, chain PB [auth V] mmCIF format, chain TB [auth Z] mmCIF format, chain VB [auth b] mmCIF format, chain WA [auth A] mmCIF format, chain XB [auth d] mmCIF format, chain YA [auth C] mmCIF format, chain ZB [auth f] mmCIF format, chain ZA [auth C] mmCIF format, chain YB [auth f] mmCIF format, chain XA [auth A] mmCIF format, chain WB [auth b] mmCIF format, chain UB [auth Z] mmCIF format, chain SB [auth X] mmCIF format, chain RB [auth X] mmCIF format, chain QB [auth V] mmCIF format, chain PC [auth v] mmCIF format, chain OC [auth v] mmCIF format, chain LC [auth r] mmCIF format, chain KC [auth r] mmCIF format, chain CC [auth j] mmCIF format, chain BC [auth h] mmCIF format, chain BB [auth F] mmCIF format, chain AB [auth D]	AB [auth D] AC [auth h] BB [auth F] BC [auth h] CB [auth F] AB [auth D], AC [auth h], BB [auth F], BC [auth h], CB [auth F], CC [auth j], DB [auth H], DC [auth j], EB [auth H], EC [auth l], FB [auth J], FC [auth n], GB [auth J], GC [auth n], HB [auth L], HC [auth o], IB [auth M], IC [auth p], JB [auth N], JC [auth p], KB [auth P], KC [auth r], LB [auth P], LC [auth r], MB [auth Q], MC [auth t], NB [auth R], NC [auth t], OB [auth U], OC [auth v], PB [auth V], PC [auth v], QB [auth V], RB [auth X], SB [auth X], TB [auth Z], UB [auth Z], VB [auth b], WA [auth A], WB [auth b], XA [auth A], XB [auth d], YA [auth C], YB [auth f], ZA [auth C], ZB [auth f]	~{N}4-(phenylmethyl)-~{N}4-[2-[3-(2-piperazin-1-ylpyrimidin-5-yl)phenyl]phenyl]pyrimidine-2,4-diamine C₃₁ H₃₀ N₈ FRBABIFCTILEGV-UHFFFAOYSA-N		Interactions Focus chain AB [auth D] Focus chain AC [auth h] Focus chain BB [auth F] Focus chain BC [auth h] Focus chain CB [auth F] Focus chain CC [auth j] Focus chain DB [auth H] Focus chain DC [auth j] Focus chain EB [auth H] Focus chain EC [auth l] Focus chain FB [auth J] Focus chain FC [auth n] Focus chain GB [auth J] Focus chain GC [auth n] Focus chain HB [auth L] Focus chain HC [auth o] Focus chain IB [auth M] Focus chain IC [auth p] Focus chain JB [auth N] Focus chain JC [auth p] Focus chain KB [auth P] Focus chain KC [auth r] Focus chain LB [auth P] Focus chain LC [auth r] Focus chain MB [auth Q] Focus chain MC [auth t] Focus chain NB [auth R] Focus chain NC [auth t] Focus chain OB [auth U] Focus chain OC [auth v] Focus chain PB [auth V] Focus chain PC [auth v] Focus chain QB [auth V] Focus chain RB [auth X] Focus chain SB [auth X] Focus chain TB [auth Z] Focus chain UB [auth Z] Focus chain VB [auth b] Focus chain WA [auth A] Focus chain WB [auth b] Focus chain XA [auth A] Focus chain XB [auth d] Focus chain YA [auth C] Focus chain YB [auth f] Focus chain ZA [auth C] Focus chain ZB [auth f] Interactions & Density Focus chain AB [auth D] Focus chain AC [auth h] Focus chain BB [auth F] Focus chain BC [auth h] Focus chain CB [auth F] Focus chain CC [auth j] Focus chain DB [auth H] Focus chain DC [auth j] Focus chain EB [auth H] Focus chain EC [auth l] Focus chain FB [auth J] Focus chain FC [auth n] Focus chain GB [auth J] Focus chain GC [auth n] Focus chain HB [auth L] Focus chain HC [auth o] Focus chain IB [auth M] Focus chain IC [auth p] Focus chain JB [auth N] Focus chain JC [auth p] Focus chain KB [auth P] Focus chain KC [auth r] Focus chain LB [auth P] Focus chain LC [auth r] Focus chain MB [auth Q] Focus chain MC [auth t] Focus chain NB [auth R] Focus chain NC [auth t] Focus chain OB [auth U] Focus chain OC [auth v] Focus chain PB [auth V] Focus chain PC [auth v] Focus chain QB [auth V] Focus chain RB [auth X] Focus chain SB [auth X] Focus chain TB [auth Z] Focus chain UB [auth Z] Focus chain VB [auth b] Focus chain WA [auth A] Focus chain WB [auth b] Focus chain XA [auth A] Focus chain XB [auth d] Focus chain YA [auth C] Focus chain YB [auth f] Focus chain ZA [auth C] Focus chain ZB [auth f]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.300 (Depositor), 0.304 (DCC)
R-Value Work: 0.211 (Depositor), 0.213 (DCC)
R-Value Observed: 0.211 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.888	α = 97.57
b = 118.348	β = 94.31
c = 186.747	γ = 98.75

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
REFMAC	refinement

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2017-03-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-03-29
Type: Initial release
Version 1.1: 2017-04-12
Changes: Database references
Version 1.2: 2017-05-10
Changes: Database references
Version 1.3: 2019-02-20
Changes: Advisory, Data collection, Derived calculations
Version 1.4: 2024-11-13
Changes: Data collection, Database references, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

5MU8 | pdb_00005mu8

HUMAN TNF-ALPHA IN COMPLEX WITH JNJ525

Literature

Structural Basis of Small-Molecule Aggregate Induced Inhibition of a Protein-Protein Interaction.

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Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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