Structure of PDB 3t1d Chain A Binding Site BS01

Receptor Information

>3t1d Chain A (length=175) Species: 9606 (Homo sapiens)

STSDLIPAPPLSKVPLQQNFQDNQFQGKWYVVGLAGNAILREDKDPQKMY
ATIYELKEDKSYNVTSVLFRKKKCDYAIATFVPGSQPGEFTLGNIKSYPG
LTSFLVRVVSTNYNQHAMVFFKKVSQNREYFKITLYGRTKELTSELKENF
IRFSKSLGLPENHIVFPVPIDQCID

Ligand information

• Ligand ID: TD1
• InChI: InChI=1S/C13H16N2O8/c14-7(4-16)13(22)23-5-8(12(20)21)15-11(19)6-2-1-3-9(17)10(6)18/h1-3,7-8,16-18H,4-5,14H2,(H,15,19)(H,20,21)/t7-,8-/m0/s1
• InChIKey: NNOZTAPXJBUXBD-YUMQZZPRSA-N
• SMILES:
  CACTVS 3.370: N[C@@H](CO)C(=O)OC[C@H](NC(=O)c1cccc(O)c1O)C(O)=O
  CACTVS 3.370: N[CH](CO)C(=O)OC[CH](NC(=O)c1cccc(O)c1O)C(O)=O
  OpenEye OEToolkits 1.7.2: c1cc(c(c(c1)O)O)C(=O)NC(COC(=O)C(CO)N)C(=O)O
  OpenEye OEToolkits 1.7.2: c1cc(c(c(c1)O)O)C(=O)N[C@@H](COC(=O)[C@H](CO)N)C(=O)O
  ACDLabs 12.01: O=C(O)C(NC(=O)c1cccc(O)c1O)COC(=O)C(N)CO
• Formula: C13 H16 N2 O8
• Name: O-[(2S)-2-amino-3-hydroxypropanoyl]-N-(2,3-dihydroxybenzoyl)-L-serine
• ZINC: ZINC000095920670
• PDB chain: 3t1d Chain A Residue 186

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3t1d Parsing the functional specificity of Siderocalin/Lipocalin 2/NGAL for siderophores and related small-molecule ligands.
• Resolution: 2.3 Å
• Binding residue (original residue number in PDB): A40 I41 F123 K125 F133 K134
• Binding residue (residue number reindexed from 1): A38 I39 F121 K123 F131 K132
• Annotation score: 1

Gene Ontology

Molecular Function

• GO:0036094 small molecule binding

External links

• PDB: RCSB:3t1d, PDBe:3t1d, PDBj:3t1d
• PDBsum: 3t1d
• PubMed: 32647813
• UniProt: P80188|NGAL_HUMAN Neutrophil gelatinase-associated lipocalin (Gene Name=LCN2)