Structure of PDB 8sge Chain B Binding Site BS01

Receptor Information

>8sge Chain B (length=325) Species: 9606 (Homo sapiens)

ACPAERSGHVAVSDGRHMFVWGGYKSNDFYLPREELWIYNMETGRWKKIN
TEGDVPPSMSGSCAVCVDRVLYLFGGHHSRGNTNKFYMLDSRSVLQWERI
DCQGIPPSSKDKLGVWVYKNKLIFFGGYGYLPEDKVLGTFEFDETSFWNS
SHPRGWNDHVHILDTETFTWSQPITTGKAPSPRAAHACATVGNRGFVFGG
RYRDARMNDLHYLNLDTWEWNELIPQGICPVGRSWHSLTPVSSDHLFLFG
GFTTDKQPLSDAWTYCISKNEWIQFNHPYTEKPRLWHTACASDEGEVIVF
GGCANNLLVHHRAAHSNEILIFSVQ

Ligand information

• Ligand ID: ZWS
• InChI: InChI=1S/C23H29N3O7/c1-4-15(2)18-11-16-7-8-24(23(31)33-10-9-32-3)13-19(16)26(22(18)30)17-5-6-20(27)25(12-17)14-21(28)29/h5-6,11-12,15H,4,7-10,13-14H2,1-3H3,(H,28,29)/t15-/m1/s1
• InChIKey: XFTKAVIYFGOXSI-OAHLLOKOSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: CCC(C)C1=CC2=C(CN(CC2)C(=O)OCCOC)N(C1=O)C3=CN(C(=O)C=C3)CC(=O)O
  OpenEye OEToolkits 2.0.7: CC[C@@H](C)C1=CC2=C(CN(CC2)C(=O)OCCOC)N(C1=O)C3=CN(C(=O)C=C3)CC(=O)O
  CACTVS 3.385: CC[C@@H](C)C1=CC2=C(CN(CC2)C(=O)OCCOC)N(C1=O)C3=CN(CC(O)=O)C(=O)C=C3
  ACDLabs 12.01: O=C(O)CN1C=C(C=CC1=O)N1C(=O)C(=CC=2CCN(CC1=2)C(=O)OCCOC)C(C)CC
  CACTVS 3.385: CC[CH](C)C1=CC2=C(CN(CC2)C(=O)OCCOC)N(C1=O)C3=CN(CC(O)=O)C(=O)C=C3
• Formula: C23 H29 N3 O7
• Name: [(5P)-5-{3-[(2R)-butan-2-yl]-7-[(2-methoxyethoxy)carbonyl]-2-oxo-5,6,7,8-tetrahydro-1,7-naphthyridin-1(2H)-yl}-2-oxopyridin-1(2H)-yl]acetic acid
• PDB chain: 8sge Chain B Residue 405

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8sge Structure-based discovery and characterization of small molecule ligands and PROTAC degraders that co-opt the E3 ligase KLHDC2 for targeted protein degradation
• Resolution: 1.509 Å
• Binding residue (original residue number in PDB): K147 Y163 W191 R236 R241 S269 W270 L343 H345
• Binding residue (residue number reindexed from 1): K112 Y128 W156 R201 R206 S234 W235 L308 H310
• Annotation score: 1

External links

• PDB: RCSB:8sge, PDBe:8sge, PDBj:8sge
• PDBsum: 8sge
• PubMed: 38177675
• UniProt: Q9Y2U9|KLDC2_HUMAN Kelch domain-containing protein 2 (Gene Name=KLHDC2)