5MU8

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
R-Value Work: 0.211
R-Value Observed: 0.211

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 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 of 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
Modelled Residue Count: 6,955
Deposited Residue Count: 7,632
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% 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 AB [auth D] SDF format, chain AC [auth h] SDF format, chain BB [auth F] SDF format, chain BC [auth h] SDF format, chain CB [auth F] SDF format, chain CC [auth j] 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 KC [auth r] SDF format, chain LB [auth P] SDF format, chain LC [auth r] 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 OC [auth v] SDF format, chain PB [auth V] SDF format, chain PC [auth v] SDF format, chain QB [auth V] SDF format, chain RB [auth X] SDF format, chain SB [auth X] SDF format, chain TB [auth Z] SDF format, chain UB [auth Z] SDF format, chain VB [auth b] SDF format, chain WA [auth A] SDF format, chain WB [auth b] SDF format, chain XA [auth A] SDF format, chain XB [auth d] SDF format, chain YA [auth C] SDF format, chain YB [auth f] SDF format, chain ZA [auth C] SDF format, chain ZB [auth f] MOL2 format, chain AB [auth D] MOL2 format, chain AC [auth h] MOL2 format, chain BB [auth F] MOL2 format, chain BC [auth h] MOL2 format, chain CB [auth F] MOL2 format, chain CC [auth j] 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 KC [auth r] MOL2 format, chain LB [auth P] MOL2 format, chain LC [auth r] 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 OC [auth v] MOL2 format, chain PB [auth V] MOL2 format, chain PC [auth v] MOL2 format, chain QB [auth V] MOL2 format, chain RB [auth X] MOL2 format, chain SB [auth X] MOL2 format, chain TB [auth Z] MOL2 format, chain UB [auth Z] MOL2 format, chain VB [auth b] MOL2 format, chain WA [auth A] MOL2 format, chain WB [auth b] MOL2 format, chain XA [auth A] MOL2 format, chain XB [auth d] MOL2 format, chain YA [auth C] MOL2 format, chain YB [auth f] MOL2 format, chain ZA [auth C] MOL2 format, chain ZB [auth f]	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]

Binding Affinity Annotations
ID	Source	Binding Affinity
JNI	BindingDB: 5MU8	IC50: min: 1100, max: 1200 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.300
R-Value Work: 0.211
R-Value Observed: 0.211
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

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