2AZ5: TNF-alpha with a small molecule inhibitor

Crystal Structure of TNF-alpha with a small molecule inhibitor. Determined by X-ray diffraction at 2.1 Å resolution. Released 29 Nov 2005.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Homo sapiens
Chains: 4
Atoms: 4,500
Mol. weight: 66.74 kDa
Ligands: 307
Released: 29 Nov 2005

Explore 2AZ5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2AZ5 contains 6 α-helices and 48 β-strands across 4 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	37-38	2	1
β-strand	42-43	2	2
β-strand	48-49	2	2
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
α-helix	147-149	3
β-strand	151-155	5	1

Chain B: 1 helix, 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	90-98	9	4
β-strand	113-126	14	3
β-strand	131-136	6	4
α-helix	139-141	3
β-strand	142	1	3
β-strand	151-155	5	3

Chain C: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	13-18	6	5
β-strand	28-29	2	5
β-strand	37-38	2	5
β-strand	42-44	3	6
β-strand	47-49	3	6
β-strand	54-66	13	5
β-strand	76-83	8	6
β-strand	90-98	9	6
β-strand	114-126	13	5
β-strand	131-136	6	6
α-helix	139-141	3
β-strand	142	1	5
β-strand	151-155	5	5

Chain D: 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	7
β-strand	47-49	3	7
β-strand	54-67	14	3
β-strand	76-84	9	7
β-strand	87-98	12	7
α-helix	112	1
β-strand	113-126	14	3
β-strand	131-136	6	7
α-helix	139-141	3
β-strand	142	1	3
β-strand	151-155	5	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tumor necrosis factor (TNF-alpha) (Tumor necrosis factor ligand superfamily member 2) (TNF-a)…	A, B, C, D	protein	148	Homo sapiens	P01375 (AlphaFold model)

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

>2AZ5_1 Tumor necrosis factor (TNF-alpha) (Tumor necrosis factor ligand superfamily member 2) (TNF-a) (Cachectin) [Contains: Tumor necrosis factor, membrane form; Tumor necrosis factor, soluble form] (chains A, B, C, D)
DKPVAHVVANPQAEGQLQWLNRRANALLANGVELRDNQLVVPSEGLYLIYSQVLFKGQGC
PSTHVLLTHTISRIAVSYQTKVNLLSAIKSPCQRETPEGAEAKPWYEPIYLGGVFQLEKG
DRLSAEINRPDYLDFAESGQVYFGIIAL

Ligands and cofactors

ID	Name	Formula	Copies
307	6,7-dimethyl-3-[(METHYL{2-[METHYL({1-[3-(trifluoromethyl)phenyl]-1H-indol-3-yl}…	C32 H32 F3 N3 O2	2

Primary citation

Small-molecule inhibition of TNF-alpha. He, M.M., Smith, A.S., Oslob, J.D. et al. Science (2005) 310:1022-1025. DOI 10.1126/science.1116304 · 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
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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