Structure of PDB 4k41 Chain A Binding Site BS03

Receptor Information

>4k41 Chain A (length=363) Species: 9986 (Oryctolagus cuniculus)

TTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQKDSYVGDEAQSKR
GILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNP
KANREKMTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHN
VPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREIVRDI
KEKLCYVALDFENEMATAASSSSLEKSYELPDGQVITIGNERFRCPETLF
QPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVMSGGTTMYPGIADR
MQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWITKQEY
DEAGPSIVHRKCF

Ligand information

• Ligand ID: KAB
• InChI: InChI=1S/C48H75N5O14/c1-27-19-33(66-48(49)58)21-43(57)67-41(22-40(60-9)28(2)15-16-37(55)30(4)44(61-10)29(3)17-18-53(7)26-54)32(6)39(59-8)13-12-14-42-50-35(24-63-42)46-52-36(25-65-46)47-51-34(23-64-47)45(62-11)31(5)38(56)20-27/h12,14,17-18,23-25,27-33,38-41,44-45,48,54,56,58H,13,15-16,19-22,26,49H2,1-11H3/b14-12+,18-17+/t27-,28-,29+,30-,31-,32+,33-,38-,39-,40-,41-,44+,45+,48+/m0/s1
• InChIKey: XYKNXOJYKRVXBX-ZAUPHERQSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: C[C@H]1C[C@@H](CC(=O)O[C@H]([C@@H]([C@H](C\C=C\c2nc(co2)-c3nc(co3)-c4nc(co4)[C@@H]([C@H]([C@H](C1)O)C)OC)OC)C)C[C@@H]([C@@H](C)CCC(=O)[C@H](C)[C@@H]([C@H](C)\C=C\N(C)CO)OC)OC)O[C@H](N)O
  OpenEye OEToolkits 1.5.0: CC1CC(CC(=O)OC(C(C(CC=Cc2nc(co2)-c3nc(co3)-c4nc(co4)C(C(C(C1)O)C)OC)OC)C)CC(C(C)CCC(=O)C(C)C(C(C)C=CN(C)CO)OC)OC)OC(N)O
  ACDLabs 10.04: O=C(C(C)C(OC)C(\C=C\N(C)CO)C)CCC(C)C(OC)CC4OC(=O)CC(OC(O)N)CC(C)CC(O)C(C)C(OC)c1nc(oc1)c2nc(oc2)c3nc(oc3)C=CCC(OC)C4C
  CACTVS 3.341: CO[CH]1CC=Cc2occ(n2)c3occ(n3)c4occ(n4)[CH](OC)[CH](C)[CH](O)C[CH](C)C[CH](CC(=O)O[CH](C[CH](OC)[CH](C)CCC(=O)[CH](C)[CH](OC)[CH](C)C=CN(C)CO)[CH]1C)O[CH](N)O
  CACTVS 3.341: CO[C@H]1C/C=C/c2occ(n2)c3occ(n3)c4occ(n4)[C@H](OC)[C@@H](C)[C@@H](O)C[C@@H](C)C[C@@H](CC(=O)O[C@@H](C[C@H](OC)[C@@H](C)CCC(=O)[C@H](C)[C@H](OC)[C@H](C)\C=C\N(C)CO)[C@@H]1C)O[C@H](N)O
• Formula: C48 H75 N5 O14
• Name: KABIRAMIDE C
• DrugBank: DB03616
• ZINC: ZINC000263621247
• PDB chain: 4k41 Chain A Residue 404

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4k41 Structural and biochemical studies of actin in complex with synthetic macrolide tail analogues.
• Resolution: 1.4 Å
• Binding residue (original residue number in PDB): D25 Y143 A144 G146 R147 G168 Y169 E334 I341 I345 S348 F375
• Binding residue (residue number reindexed from 1): D21 Y131 A132 G134 R135 G156 Y157 E322 I329 I333 S336 F363
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 3.6.4.-

Gene Ontology

Molecular Function

• GO:0000287 magnesium ion binding
• GO:0003785 actin monomer binding
• GO:0005509 calcium ion binding
• GO:0005515 protein binding
• GO:0005523 tropomyosin binding
• GO:0005524 ATP binding
• GO:0016787 hydrolase activity
• GO:0019904 protein domain specific binding
• GO:0031013 troponin I binding
• GO:0031432 titin binding
• GO:0032036 myosin heavy chain binding
• GO:0042802 identical protein binding
• GO:0048306 calcium-dependent protein binding
• GO:0140660 cytoskeletal motor activator activity

Biological Process

• GO:0010628 positive regulation of gene expression
• GO:0030041 actin filament polymerization
• GO:0030240 skeletal muscle thin filament assembly
• GO:0048741 skeletal muscle fiber development
• GO:0051017 actin filament bundle assembly
• GO:0090131 mesenchyme migration

Cellular Component

• GO:0001725 stress fiber
• GO:0005737 cytoplasm
• GO:0005856 cytoskeleton
• GO:0005865 striated muscle thin filament
• GO:0005884 actin filament
• GO:0030027 lamellipodium
• GO:0030175 filopodium
• GO:0031941 filamentous actin
• GO:0032432 actin filament bundle
• GO:0044297 cell body
• GO:0098723 skeletal muscle myofibril

External links

• PDB: RCSB:4k41, PDBe:4k41, PDBj:4k41
• PDBsum: 4k41
• PubMed: 25047814
• UniProt: P68135|ACTS_RABIT Actin, alpha skeletal muscle (Gene Name=ACTA1)