9OJY: TNF alpha

Crystal structure of TNF alpha in complex with compound 3. Determined by X-ray diffraction at 2.16 Å resolution. Released 23 Jul 2025.

Method: X-ray diffraction
Resolution: 2.16 Å
Organism: Homo sapiens
Chains: 6
Atoms: 6,234
Mol. weight: 105.97 kDa
Ligands: A1CBZ
Released: 23 Jul 2025

Explore 9OJY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9OJY contains 10 α-helices and 70 β-strands across 6 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	13-18	6	1
β-strand	28-29	2	1
β-strand	36-38	3	1
β-strand	42-44	3	2
β-strand	47-49	3	2
α-helix	50	1
β-strand	54-66	13	1
β-strand	76-83	8	2
β-strand	90-98	9	2
β-strand	114-126	13	1
β-strand	131-136	6	2
α-helix	139-141	3
β-strand	142	1	1
β-strand	151-156	6	1

Chain B: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	13-18	6	3
β-strand	28-29	2	3
β-strand	42-44	3	4
β-strand	47-49	3	4
β-strand	54-66	13	3
β-strand	76-83	8	4
β-strand	90-98	9	4
β-strand	114-126	13	3
β-strand	131-136	6	4
α-helix	139-141	3
β-strand	142	1	3
α-helix	147-149	3
β-strand	151-156	6	3

Chain C: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	13-18	6	5
β-strand	28-29	2	5
β-strand	36-38	3	5
β-strand	42-44	3	6
β-strand	47-49	3	6
α-helix	50	1
β-strand	54-66	13	5
β-strand	76-83	8	6
β-strand	91-98	8	6
α-helix	112-113	2
β-strand	114-126	13	5
β-strand	131-136	6	6
α-helix	139-141	3
β-strand	142	1	5
β-strand	151-156	6	5

Chain D: 1 helix, 13 β-strands

Element	Residues	Length	Sheet
β-strand	13-18	6	2
β-strand	28-29	2	2
β-strand	31	1	2
β-strand	36-38	3	2
β-strand	42-44	3	7
β-strand	47-49	3	7
β-strand	54-66	13	2
β-strand	76-83	8	7
β-strand	92-98	7	7
β-strand	114-126	13	2
β-strand	131-136	6	7
α-helix	139-141	3
β-strand	142	1	2
β-strand	151-156	6	2

Chain E: 1 helix, 10 β-strands

Element	Residues	Length	Sheet
β-strand	13-18	6	8
β-strand	28-29	2	8
β-strand	42-44	3	9
β-strand	47-49	3	9
α-helix	50	1
β-strand	54-66	13	8
β-strand	76-83	8	9
β-strand	90-98	9	9
β-strand	114-126	13	8
β-strand	131-136	6	9
β-strand	151-156	6	8

Chain F: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	13-18	6	10
β-strand	28-29	2	10
β-strand	36-38	3	10
β-strand	42-44	3	11
β-strand	47-49	3	11
β-strand	54-66	13	10
β-strand	76-83	8	11
β-strand	90-98	9	11
β-strand	114-126	13	10
β-strand	131-136	6	11
α-helix	139-141	3
β-strand	142	1	10
β-strand	151-156	6	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tumor necrosis factor	A, B, C, D, E, F	protein	158	Homo sapiens	P01375 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F), FASTA

>9OJY_1 Tumor necrosis factor (chains A, B, C, D, E, F)
MVRSSSRTPSDKPVAHVVANPQAEGQLQWLNRRANALLANGVELRDNQLVVPSEGLYLIY
SQVLFKGQGCPSTHVLLTHTISRIAVSYQTKVNLLSAIKSPCQRETPEGAEAKPWYEPIY
LGGVFQLEKGDRLSAEINRPDYLDFAESGQVYFGIIAL

Ligands and cofactors

ID	Name	Formula	Copies
A1CBZ	(6R,13R,14S)-1-(difluoromethoxy)-11-[2-(2-hydroxypropan-2-yl)pyrimidin-5-yl]-7H…	C24 H20 F2 N6 O3	2

Primary citation

Discovery of Orally Efficacious Bridged Piperazines as smTNF Modulators. Bian, Z., Schmidt, R.G., Wilson, N.S. et al. J Med Chem (2025) 68:14357-14383. DOI 10.1021/acs.jmedchem.5c00323 · PubMed

Other PDB entries of the same protein (UniProt P01375 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9OJO 1.36 Å, Crystal structure of TNF alpha in complex with compound 1
5UUI 1.4 Å, Crystal Structure of Spin-Labeled T77C TNFa
4Y6O 1.6 Å, Human SIRT2 in complex with myristoylated peptide (TNF-alphaK20myr)
2E7A 1.8 Å, TNF Receptor Subtype One-selective TNF Mutant with Antagonistic Activity
4TSV 1.8 Å, High resolution crystal structure of a human tnf-alpha mutant
9OJS 1.85 Å, Crystal structure of TNF alpha in complex with compound 4
5M2J 1.9 Å, Complex between human TNF alpha and Llama VHH2
9BN7 1.92 Å, X-ray crystal structure of TNFa-VNAR C4 complex
2AZ5 2.1 Å, Crystal Structure of TNF-alpha with a small molecule inhibitor
3L9J 2.1 Å, Selection of a novel highly specific TNFalpha antagonist: Insight from the crystal…
7JRA 2.1 Å, HUMAN TNF-ALPHA IN COMPLEX WITH 2-[5-(3-chloro-4-{[(1R)-1-(2-fluorophenyl)ethyl]amino}qui…
5M2I 2.15 Å, Structure of human Tumor Necrosis Factor (TNF) in complex with the Llama VHH1

Browse structure collections

About this viewer

MolViewer shows 9OJY directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.