Structure of PDB 5bmf Chain L Binding Site BS01

Receptor Information

>5bmf Chain L (length=216) Species: 9606 (Homo sapiens)

DVVMTQSPLSLPVTLGQPASISCRSSQSIVYNNRYTYLEWFQQRPGQSPR
LLIYGVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCYQGTHAP
YTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAK
VQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACE
VTHQGLSSPVTKSFNR

Ligand information

• Ligand ID: 4TJ
• InChI: InChI=1S/C50H66N8O12S2/c1-8-57-38-24-22-34(71(63,64)65)32-37(38)50(4,5)40(57)16-11-9-12-17-41-49(2,3)36-23-21-35(72(66,67)68)33-39(36)58(41)27-14-10-13-19-43(59)51-25-28-69-30-31-70-29-26-52-44(60)20-15-18-42-53-45-46(54-42)55(6)48(62)56(7)47(45)61/h9,11-12,16-17,21-24,32-33H,8,10,13-15,18-20,25-31H2,1-7H3,(H4-,51,52,53,54,59,60,61,63,64,65,66,67,68)
• InChIKey: PHMVJTFYMDAUCS-UHFFFAOYSA-N
• SMILES:
  ACDLabs 12.01: N1(C(c6c(N(C)C1=O)nc(CCCC(NCCOCCOCCNC(=O)CCCCCN2/C(C(c3c2cc(cc3)S(O)(=O)=O)(C)C)=C\C=C\C=C\C4=[N+](c5ccc(cc5C4(C)C)S(=O)([O-])=O)CC)=O)n6)=O)C
  CACTVS 3.385: CC[N+]1=C(C=CC=CC=C2N(CCCCCC(=O)NCCOCCOCCNC(=O)CCCc3[nH]c4C(=O)N(C)C(=O)N(C)c4n3)c5cc(ccc5C2(C)C)[S](O)(=O)=O)C(C)(C)c6cc(ccc16)[S]([O-])(=O)=O
  OpenEye OEToolkits 1.9.2: CC[N+]1=C(C(c2c1ccc(c2)S(=O)(=O)[O-])(C)C)C=CC=CC=C3C(c4ccc(cc4N3CCCCCC(=O)NCCOCCOCCNC(=O)CCCc5[nH]c6c(n5)N(C(=O)N(C6=O)C)C)S(=O)(=O)O)(C)C
• Formula: C50 H66 N8 O12 S2
• PDB chain: 5bmf Chain H Residue 1201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5bmf MoFvAb: Modeling the Fv region of antibodies.
• Resolution: 2.8 Å
• Binding residue (original residue number in PDB): Y581 Y597 Y751 G753 Y798
• Binding residue (residue number reindexed from 1): Y31 Y37 Y94 G96 Y101
• Annotation score: 1

External links

• PDB: RCSB:5bmf, PDBe:5bmf, PDBj:5bmf
• PDBsum: 5bmf
• PubMed: 26176812