Structure of PDB 4ocx Chain L Binding Site BS01

Receptor Information

>4ocx Chain L (length=214) Species: 10090 (Mus musculus)

DVLLTQIPLSLPVSLGDQASISCRSSQSIVHSNGNTYLEWYLQKPGQSPK
LLIYKVSTRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVP
LTFGAGTQLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDIN
VKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCE
ATHKTSPIVKSFNR

Ligand information

• Ligand ID: MT1
• InChI: InChI=1S/C20H22N8O5/c1-28(9-11-8-23-17-15(24-11)16(21)26-20(22)27-17)12-4-2-10(3-5-12)18(31)25-13(19(32)33)6-7-14(29)30/h2-5,8,13H,6-7,9H2,1H3,(H,25,31)(H,29,30)(H,32,33)(H4,21,22,23,26,27)/p+1/t13-/m0/s1
• InChIKey: FBOZXECLQNJBKD-ZDUSSCGKSA-O
• SMILES:
  OpenEye OEToolkits 1.5.0: CN(Cc1cnc2c(n1)c(nc([nH+]2)N)N)c3ccc(cc3)C(=O)NC(CCC(=O)O)C(=O)O
  CACTVS 3.341: CN(Cc1cnc2[nH+]c(N)nc(N)c2n1)c3ccc(cc3)C(=O)N[C@@H](CCC(O)=O)C(O)=O
  CACTVS 3.341: CN(Cc1cnc2[nH+]c(N)nc(N)c2n1)c3ccc(cc3)C(=O)N[CH](CCC(O)=O)C(O)=O
  ACDLabs 10.04: O=C(O)C(NC(=O)c1ccc(cc1)N(C)Cc2nc3c(nc2)[nH+]c(nc3N)N)CCC(=O)O
  OpenEye OEToolkits 1.5.0: CN(Cc1cnc2c(n1)c(nc([nH+]2)N)N)c3ccc(cc3)C(=O)N[C@@H](CCC(=O)O)C(=O)O
• Formula: C20 H23 N8 O5
• Name: N-(4-{[(2,4-DIAMINOPTERIDIN-1-IUM-6-YL)METHYL](METHYL)AMINO}BENZOYL)-L-GLUTAMIC ACID;
  METHOTREXATE PROTONATED AT N1
• PDB chain: 4ocx Chain L Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4ocx Water channel in the binding site of a high affinity anti-methotrexate antibody.
• Resolution: 2.39 Å
• Binding residue (original residue number in PDB): H31 Y37 E39 F94 G96 L101
• Binding residue (residue number reindexed from 1): H31 Y37 E39 F94 G96 L101
• Annotation score: 1
• Binding affinity: MOAD: Kd~3.6pM
  PDBbind-CN: -logKd/Ki=11.44,Kd~3.6pM

Gene Ontology

Molecular Function

• GO:0046872 metal ion binding

External links

• PDB: RCSB:4ocx, PDBe:4ocx, PDBj:4ocx
• PDBsum: 4ocx
• PubMed: 24832237
• UniProt: A2NHM3