Structure of PDB 4mdk Chain D Binding Site BS01

Receptor Information

>4mdk Chain D (length=157) Species: 9606 (Homo sapiens)

PSSQKALLLELKGLQEEPVEGFRVTLVDEGDLYNWEVAIFGPPNTYYEGG
YFKARLKFPIDYPYSPPAFRFLTKMWHPNIYETGDVCNPTQNVRTILLSV
ISLLNEPNTFSPANVDASVMYRKWKESKGKDREYTDIIRKQVLGTKVDAE
RDGVKVP

Ligand information

• Ligand ID: U94
• InChI: InChI=1S/C20H21Cl2NO6/c1-29-10-17(24)23-16(18(25)19(26)20(27)28)6-11-2-4-12(5-3-11)13-7-14(21)9-15(22)8-13/h2-5,7-9,16,18-19,25-26H,6,10H2,1H3,(H,23,24)(H,27,28)/t16-,18-,19+/m0/s1
• InChIKey: NTCBTNCWNRCBGX-YTQUADARSA-N
• SMILES:
  ACDLabs 12.01: Clc2cc(c1ccc(cc1)CC(NC(=O)COC)C(O)C(O)C(=O)O)cc(Cl)c2
  OpenEye OEToolkits 1.7.2: COCC(=O)NC(Cc1ccc(cc1)c2cc(cc(c2)Cl)Cl)C(C(C(=O)O)O)O
  OpenEye OEToolkits 1.7.2: COCC(=O)N[C@@H](Cc1ccc(cc1)c2cc(cc(c2)Cl)Cl)[C@@H]([C@H](C(=O)O)O)O
  CACTVS 3.370: COCC(=O)N[CH](Cc1ccc(cc1)c2cc(Cl)cc(Cl)c2)[CH](O)[CH](O)C(O)=O
  CACTVS 3.370: COCC(=O)N[C@@H](Cc1ccc(cc1)c2cc(Cl)cc(Cl)c2)[C@H](O)[C@@H](O)C(O)=O
• Formula: C20 H21 Cl2 N O6
• Name: 4,5-dideoxy-5-(3',5'-dichlorobiphenyl-4-yl)-4-[(methoxyacetyl)amino]-L-arabinonic acid
• ChEMBL: CHEMBL1738913
• ZINC: ZINC000066166106
• PDB chain: 4mdk Chain D Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4mdk E2 enzyme inhibition by stabilization of a low-affinity interface with ubiquitin.
• Resolution: 2.6095 Å
• Binding residue (original residue number in PDB): I45 P48 T51 Y52 Y53 F58 L131 N132 W151
• Binding residue (residue number reindexed from 1): I39 P42 T45 Y46 Y47 F52 L104 N105 W124
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): C93
• Catalytic site (residue number reindexed from 1): C87
• Enzyme Commision number: 2.3.2.23: E2 ubiquitin-conjugating enzyme.
  2.3.2.24: (E3-independent) E2 ubiquitin-conjugating enzyme.

External links

• PDB: RCSB:4mdk, PDBe:4mdk, PDBj:4mdk
• PDBsum: 4mdk
• PubMed: 24316736
• UniProt: P49427|UB2R1_HUMAN Ubiquitin-conjugating enzyme E2 R1 (Gene Name=CDC34)