7JRA: HUMAN TNF-ALPHA

HUMAN TNF-ALPHA IN COMPLEX WITH 2-[5-(3-chloro-4-{[(1R)-1-(2-fluorophenyl)ethyl]amino}quinolin-6-yl)pyrimidin-2-yl]propan-2-ol. Determined by X-ray diffraction at 2.1 Å resolution. Released 9 Dec 2020.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Homo sapiens
Chains: 3
Atoms: 3,518
Mol. weight: 53.62 kDa
Ligands: VGY
Released: 9 Dec 2020

Explore 7JRA in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7JRA contains 9 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: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	82-85	4
β-strand	89-94	6	1
β-strand	104-105	2	1
β-strand	112-114	3	1
β-strand	118-120	3	2
β-strand	123-125	3	2
β-strand	130-143	14	1
β-strand	152-160	9	2
β-strand	163-174	12	2
α-helix	181-182	2
β-strand	189-202	14	1
β-strand	207-212	6	2
α-helix	215-217	3
β-strand	218	1	1
β-strand	227-232	6	1

Chain B: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	83-85	3
β-strand	89-94	6	3
β-strand	104-105	2	3
β-strand	112-114	3	3
β-strand	118-120	3	4
β-strand	123-125	3	4
β-strand	130-143	14	3
α-helix	149-150	2
β-strand	152-160	9	4
β-strand	165-174	10	4
β-strand	189-202	14	3
β-strand	207-212	6	4
α-helix	215-217	3
β-strand	218	1	3
β-strand	227-232	6	3

Chain C: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	89-94	6	5
β-strand	104-105	2	5
β-strand	112-114	3	5
β-strand	118-120	3	6
β-strand	123-125	3	6
α-helix	126	1
β-strand	130-143	14	5
α-helix	149-150	2
β-strand	152-159	8	6
β-strand	166-174	9	6
β-strand	189-202	14	5
β-strand	207-212	6	6
α-helix	215-217	3
β-strand	218	1	5
β-strand	227-232	6	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tumor necrosis factor	A, B, C	protein	160	Homo sapiens	P01375 (AlphaFold model)

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

>7JRA_1 Tumor necrosis factor (chains A, B, C)
GHMVRSSSRTPSDKPVAHVVANPQAEGQLQWLNRRANALLANGVELRDNQLVVPSEGLYL
IYSQVLFKGQGCPSTHVLLTHTISRIAVSYQTKVNLLSAIKSPCQRETPEGAEAKPWYEP
IYLGGVFQLEKGDRLSAEINRPDYLDFAESGQVYFGIIAL

Ligands and cofactors

ID	Name	Formula	Copies
VGY	2-[5-(3-chloro-4-{[(1R)-1-(2-fluorophenyl)ethyl]amino}quinolin-6-yl)pyrimidin-2…	C24 H22 Cl F N4 O	1

Water and common crystallization additives (GOL) are not listed.

Primary citation

Biologic-like In Vivo Efficacy with Small Molecule Inhibitors of TNF alpha Identified Using Scaffold Hopping and Structure-Based Drug Design Approaches. Xiao, H.Y., Li, N., Duan, J.J. et al. J Med Chem (2020) 63:15050-15071. DOI 10.1021/acs.jmedchem.0c01732 · 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…
5M2I 2.15 Å, Structure of human Tumor Necrosis Factor (TNF) in complex with the Llama VHH1
7KP9 2.15 Å, asymmetric hTNF-alpha

Browse structure collections

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