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- ChemComp-NEF: Nitrocefin - open form -

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Basic information

EntryDatabase: PDB chemical components / ID: NEF
NameName: Nitrocefin - open form
Synonyms: (2R)-5-[(E)-2-(2,4-dinitrophenyl)ethenyl]-2-[(1R)-2-oxidanyl-2-oxidanylidene-1-(2-thiophen-2-ylethanoylamino)ethyl]-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid

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Chemical information

Composition
Formula: C21H18N4O9S2 / Number of atoms: 54 / Formula weight: 534.519 / Formal charge: 0
Others

6hr9

Type: NON-POLYMER / PDB classification: HETAIN / Three letter code: NEF / Ideal coordinates details: Corina / Model coordinates PDB-ID: 6HR9
History
Create componentSep 26, 2018
Other modificationSep 27, 2018
Initial releaseOct 23, 2019
Modify leaving atom flagAug 24, 2021
Modify aromatic flagSep 6, 2021
External linksUniChem / ChemSpider / Wikipedia search / Google search

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Details

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SMILES

CACTVS 3.385OC(=O)[CH](NC(=O)Cc1sccc1)[CH]2NC(=C(CS2)C=Cc3ccc(cc3[N+]([O-])=O)[N+]([O-])=O)C(O)=O
OpenEye OEToolkits 2.0.7c1cc(sc1)CC(=O)NC(C2NC(=C(CS2)C=Cc3ccc(cc3[N+](=O)[O-])[N+](=O)[O-])C(=O)O)C(=O)O

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SMILES CANONICAL

CACTVS 3.385OC(=O)[C@@H](NC(=O)Cc1sccc1)[C@@H]2NC(=C(CS2)\C=C\c3ccc(cc3[N+]([O-])=O)[N+]([O-])=O)C(O)=O
OpenEye OEToolkits 2.0.7c1cc(sc1)CC(=O)N[C@@H]([C@@H]2NC(=C(CS2)/C=C/c3ccc(cc3[N+](=O)[O-])[N+](=O)[O-])C(=O)O)C(=O)O

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InChI

InChI 1.03InChI=1S/C21H18N4O9S2/c26-16(9-14-2-1-7-35-14)22-18(21(29)30)19-23-17(20(27)28)12(10-36-19)4-3-11-5-6-13(24(31)32)8-15(11)25(33)34/h1-8,18-19,23H,9-10H2,(H,22,26)(H,27,28)(H,29,30)/b4-3+/t18-,19+/m0/s1

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InChIKey

InChI 1.03PYBZXZZHQKFSGC-CZHQAMEJSA-N

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PDB entries

Showing all 3 items

PDB-6hr6:
Nitrocefin reacted with catalytic serine (Ser294) of penicillin-binding protein 3 from Pseudomonas aeruginosa

PDB-6hr9:
Nitrocefin acylation of both catalytic serines of the Y409 mutant of penicillin-binding protein 3 from P. aeruginosa

PDB-9r7e:
Cryo-EM Structure of catalytic amyloids

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