9OJO: TNF alpha

Crystal structure of TNF alpha in complex with compound 1. Determined by X-ray diffraction at 1.36 Å resolution. Released 23 Jul 2025.

Method: X-ray diffraction
Resolution: 1.36 Å
Organism: Homo sapiens
Chains: 3
Atoms: 3,539
Mol. weight: 52.89 kDa
Ligands: A1CB1
Released: 23 Jul 2025

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

Secondary structure: helices and β-sheets

9OJO contains 5 α-helices and 36 β-strands across 3 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: 1 helix, 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
β-strand	54-67	14	1
β-strand	76-84	9	2
β-strand	87-98	12	2
β-strand	113-126	14	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, 12 β-strands

Element	Residues	Length	Sheet
β-strand	13-18	6	3
β-strand	28-29	2	3
β-strand	36-38	3	3
β-strand	42-44	3	4
β-strand	47-49	3	4
β-strand	54-67	14	3
β-strand	76-83	8	4
β-strand	91-98	8	4
β-strand	113-126	14	3
β-strand	131-136	6	4
α-helix	139-141	3
β-strand	142	1	3
α-helix	144-149	6
β-strand	151-156	6	3

Chain C: 2 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
β-strand	54-67	14	5
α-helix	73-74	2
β-strand	76-83	8	6
β-strand	90-98	9	6
β-strand	113-126	14	5
β-strand	131-136	6	6
α-helix	139-141	3
β-strand	142	1	5
β-strand	151-156	6	5

Molecules and chains

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

Sequence of entity 1 (A, B, C), FASTA

>9OJO_1 Tumor necrosis factor (chains A, B, C)
MVRSSSRTPSDKPVAHVVANPQAEGQLQWLNRRANALLANGVELRDNQLVVPSEGLYLIY
SQVLFKGQGCPSTHVLLTHTISRIAVSYQTKVNLLSAIKSPCQRETPEGAEAKPWYEPIY
LGGVFQLEKGDRLSAEINRPDYLDFAESGQVYFGIIAL

Ligands and cofactors

ID	Name	Formula	Copies
A1CB1	2-{5-[(1S,10S)-1-phenyl-1,2,3,4-tetrahydropyrido[1,2-a][1,3]benzimidazol-8-yl]p…	C24 H24 N4 O	1

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:

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
7KP9 2.15 Å, asymmetric hTNF-alpha

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