Structure of PDB 4haz Chain C Binding Site BS01

Receptor Information

>4haz Chain C (length=1014) Species: 4932 (Saccharomyces cerevisiae)

AMEGILDFSNDLDIALLDQVVSTFYQGSGVQQKQAQEILTKFQDNPDAWQ
KADQILQFSTNPQSKFIALSILDKLITRKWKLLPNDHRIGIRNFVVGMII
SMCQDDEVFKTQKNLINKSDLTLVQILKQEWPQNWPEFIPELIGSSSSSV
NVCENNMIVLKLLSEEVFDFSAEQMTQAKALHLKNSMSKEFEQIFKLCFQ
VLEQGSSSSLIVATLESLLRYLHWIPYRYIYETNILELLSTKFMTSPDTR
AITLKCLTEVSNLKIPQDNDLIKRQTVLFFQNTLQQIATSVMPVTADLKA
TYANANGNDQSFLQDLAMFLTTYLARNRALLESDESLRELLLNAHQYLIQ
LSKIEERELFKTTLDYWHNLVADLFYEPLKKHIYEEICSQLRLVIIENMV
RPEEVLVVENDEGEIVREFVKESDTIQLYKSEREVLVYLTHLNVIDTEEI
MISKLARQIDGSEWSWHNINTLSWAIGSISGTMSEDTEKRFVVTVIKDLL
DLCVKKSGKDNEAVVASDIMYVVGQYPRFLKAHWNFLRTVILQLFEFMHE
THEGVQDMACDTFIKIVQKCKYHFVIQQPRESEPFIQTIIRDIQKTTADL
QPQQVHTFYKACGIIISEERSVAERNRLLSDLMQLPNMAWDTIVEQSTAN
PTLLDSETVKIIANIIKTNVAVCTSMGADFYPQLGHIYYNMLQLYRAVSS
MISAQVAAEGLIATKTPKVRGLRTIKKEILKLVETYISKARNLDDVVKVL
VEPLLNAVLEDYMNNVPDARDAEVLNCMTTVVEKVGHMIPQGVILILQSV
FECTLDMINKDFTEYPEHRVEFYKLLKVINEKSFAAFLELPPAAFKLFVD
AICWAFKHNNRDVEVNGLQIALDLVKNIERMGNVPFANEFHKNYFFIFVS
ETFFVLTDSDHKSGFSKQALLLMKLISLVYDNKISVPLYQAEVPQGTSNQ
VYLSQYLANMLSNAFPHLTSEQIASFLSALTKQCKDLVVFKGTLRDFLVQ
IKEVGGDPTDYLFA

Ligand information

• Ligand ID: LBF
• InChI: InChI=1S/C33H48O6/c1-9-28(14-15-29-24(5)13-16-31(36)39-29)19-22(3)12-10-11-21(2)17-25(6)32(37)27(8)33(38)26(7)18-23(4)20-30(34)35/h10-11,13-17,19-20,22,24-27,29,33,38H,9,12,18H2,1-8H3,(H,34,35)/b11-10+,15-14+,21-17+,23-20+,28-19-/t22-,24+,25-,26+,27-,29+,33-/m1/s1
• InChIKey: YACHGFWEQXFSBS-XYERBDPFSA-N
• SMILES:
  OpenEye OEToolkits 1.7.6: CC/C(=C/[C@H](C)C/C=C/C(=C/[C@@H](C)C(=O)[C@@H](C)[C@@H]([C@@H](C)C/C(=C/C(=O)O)/C)O)/C)/C=C/[C@H]1[C@H](C=CC(=O)O1)C
  ACDLabs 12.01: O=C(O)\C=C(/C)CC(C)C(O)C(C(=O)C(/C=C(/C=C/CC(/C=C(\C=C\C1OC(=O)C=CC1C)CC)C)C)C)C
  OpenEye OEToolkits 1.7.6: CCC(=CC(C)CC=CC(=CC(C)C(=O)C(C)C(C(C)CC(=CC(=O)O)C)O)C)C=CC1C(C=CC(=O)O1)C
  CACTVS 3.370: CCC(C=C[CH]1OC(=O)C=C[CH]1C)=C[CH](C)CC=CC(C)=C[CH](C)C(=O)[CH](C)[CH](O)[CH](C)CC(C)=CC(O)=O
  CACTVS 3.370: CCC(/C=C/[C@@H]1OC(=O)C=C[C@@H]1C)=C/[C@H](C)C/C=C/C(C)=C/[C@@H](C)C(=O)[C@@H](C)[C@H](O)[C@@H](C)CC(/C)=C/C(O)=O
• Formula: C33 H48 O6
• Name: Leptomycin B
• ChEMBL: CHEMBL486133
• ZINC: ZINC000017654252
• PDB chain: 4haz Chain C Residue 1101

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4haz Nuclear export inhibition through covalent conjugation and hydrolysis of Leptomycin B by CRM1.
• Resolution: 1.9 Å
• Binding residue (original residue number in PDB): K525 V529 L536 C539 A552 I555 F572 T575 Q579 F583
• Binding residue (residue number reindexed from 1): K489 V493 L500 C503 A516 I519 F536 T539 Q543 F547
• Annotation score: 1

Gene Ontology

Molecular Function

• GO:0005049 nuclear export signal receptor activity
• GO:0005515 protein binding
• GO:0017070 U6 snRNA binding
• GO:0030619 U1 snRNA binding
• GO:0030620 U2 snRNA binding
• GO:0030621 U4 snRNA binding
• GO:0030623 U5 snRNA binding
• GO:0031267 small GTPase binding
• GO:0061608 nuclear import signal receptor activity

Biological Process

• GO:0000055 ribosomal large subunit export from nucleus
• GO:0000056 ribosomal small subunit export from nucleus
• GO:0006406 mRNA export from nucleus
• GO:0006409 tRNA export from nucleus
• GO:0006611 protein export from nucleus
• GO:0006886 intracellular protein transport
• GO:0015031 protein transport
• GO:0034501 protein localization to kinetochore
• GO:0051168 nuclear export
• GO:0051170 import into nucleus
• GO:0071528 tRNA re-export from nucleus

Cellular Component

• GO:0000776 kinetochore
• GO:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005816 spindle pole body
• GO:0048471 perinuclear region of cytoplasm

External links

• PDB: RCSB:4haz, PDBe:4haz, PDBj:4haz
• PDBsum: 4haz
• PubMed: 23297231
• UniProt: P30822|XPO1_YEAST Exportin-1 (Gene Name=CRM1)