Structure of PDB 5m37 Chain A Binding Site BS02

Receptor Information

>5m37 Chain A (length=230) Species: 9606 (Homo sapiens)

MDKNELVQKAKLAEQAERYDDMAACMKSVTEQGAELSNEERNLLSVAYKN
VVGARRSSWRVVSSIEQKTEGAEKKQQMAREYREKIETELRDICNDVLSL
LEKFLIPNASQAESKVFYLKMKGDYYRYLAEVAAGDDKKGIVDQSQQAYQ
EAFEISKKEMQPTHPIRLGLALNFSVFYYEILNSPEKACSLAKTAFDEAI
AELDTLSEESYKDSTLIMQLLRDNLTLWTS

Ligand information

• Ligand ID: 9SZ
• InChI: InChI=1S/C42H32O8P2/c43-51(44,45)49-41-37-33-15-34(30-12-26-22-9-21(25(26)11-29(30)33)17-5-1-2-6-18(17)22)38(37)42(50-52(46,47)48)40-36-16-35(39(40)41)31-13-27-23-10-24(28(27)14-32(31)36)20-8-4-3-7-19(20)23/h1-8,11-14,21-24,33-36H,9-10,15-16H2,(H2,43,44,45)(H2,46,47,48)/t21-,22+,23+,24-,33-,34+,35+,36-
• InChIKey: BZESKQAEKFQSPD-FCODNRGNSA-N
• SMILES:
  OpenEye OEToolkits 2.0.6: c1ccc2c(c1)C3CC2c4c3cc5c(c4)C6CC5c7c6c(c8c(c7OP(=O)(O)O)C9CC8c1c9cc2c(c1)C1CC2c2c1cccc2)OP(=O)(O)O
  CACTVS 3.385: O[P](O)(=O)Oc1c2[CH]3C[CH](c4cc5[CH]6C[CH](c7ccccc67)c5cc34)c2c(O[P](O)(O)=O)c8[CH]9C[CH](c%10cc%11[CH]%12C[CH](c%13ccccc%12%13)c%11cc9%10)c18
  CACTVS 3.385: O[P](O)(=O)Oc1c2[C@@H]3C[C@@H](c4cc5[C@H]6C[C@H](c7ccccc67)c5cc34)c2c(O[P](O)(O)=O)c8[C@@H]9C[C@@H](c%10cc%11[C@H]%12C[C@H](c%13ccccc%12%13)c%11cc9%10)c18
  OpenEye OEToolkits 2.0.6: c1ccc2c(c1)[C@H]3C[C@@H]2c4c3cc5c(c4)[C@@H]6C[C@H]5c7c6c(c8c(c7OP(=O)(O)O)[C@H]9C[C@@H]8c1c9cc2c(c1)[C@@H]1C[C@H]2c2c1cccc2)OP(=O)(O)O
• Formula: C42 H32 O8 P2
• Name: (1R,5S,9S,16R,20R,24S,28S,35R)-3,22-Bis(dihydroxyphosphoryloxy)tridecacyclo[22.14.1.15,20.19,16.128,35.02,23.04,21.06,19.08,17.010,15.025,38.027,36.029,34]dotetraconta-2(23),3,6,8(17),10,12,14,18,21,25,27(36),29,31,33,37-pentadecaene
• PDB chain: 5m37 Chain D Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5m37 The Molecular Tweezer CLR01 Stabilizes a Disordered Protein-Protein Interface.
• Resolution: 2.35 Å
• Binding residue (original residue number in PDB): W59 Q67 Y179 E180
• Binding residue (residue number reindexed from 1): W59 Q67 Y179 E180
• Annotation score: 1

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0005515 protein binding
• GO:0019901 protein kinase binding
• GO:0019904 protein domain specific binding
• GO:0031625 ubiquitin protein ligase binding
• GO:0042802 identical protein binding
• GO:0044325 transmembrane transporter binding
• GO:0045296 cadherin binding
• GO:0050815 phosphoserine residue binding
• GO:0140297 DNA-binding transcription factor binding
• GO:0140311 protein sequestering activity

Biological Process

• GO:0000122 negative regulation of transcription by RNA polymerase II
• GO:0001525 angiogenesis
• GO:0003016 respiratory system process
• GO:0006468 protein phosphorylation
• GO:0006605 protein targeting
• GO:0007165 signal transduction
• GO:0008039 synaptic target recognition
• GO:0008104 protein localization
• GO:0030324 lung development
• GO:0031647 regulation of protein stability
• GO:0035148 tube formation
• GO:0042149 cellular response to glucose starvation
• GO:0043066 negative regulation of apoptotic process
• GO:0043067 regulation of programmed cell death
• GO:0045824 negative regulation of innate immune response
• GO:0051683 establishment of Golgi localization
• GO:0070371 ERK1 and ERK2 cascade
• GO:0070372 regulation of ERK1 and ERK2 cascade
• GO:0090128 regulation of synapse maturation
• GO:0090168 Golgi reassembly
• GO:1900181 negative regulation of protein localization to nucleus
• GO:1904262 negative regulation of TORC1 signaling

Cellular Component

• GO:0005615 extracellular space
• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0005925 focal adhesion
• GO:0031982 vesicle
• GO:0042470 melanosome
• GO:0070062 extracellular exosome
• GO:0072562 blood microparticle
• GO:0098686 hippocampal mossy fiber to CA3 synapse
• GO:0098978 glutamatergic synapse

External links

• PDB: RCSB:5m37, PDBe:5m37, PDBj:5m37
• PDBsum: 5m37
• PubMed: 29039919
• UniProt: P63104|1433Z_HUMAN 14-3-3 protein zeta/delta (Gene Name=YWHAZ)