Structure of PDB 9b0e Chain A Binding Site BS02

Receptor Information

>9b0e Chain A (length=821) Species: 759272 (Thermochaetoides thermophila DSM 1495) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

TVDSRIPTLIRNGLQTKKRSFFVVVGDHAKEAIVHLYYIMSSMDVRQNKS
VLWAYKKPFELFISLNDIRYCYYKETDKILGNTYGMCILQDFEAITPNIL
ARTIETVEGGGLVVLLLKGMTSLKQLYTMTMDVHARYRTEAHDDVIARFN
ERFLLSLGSCESCLVIDDELNVLPISGGKGVKPLPPPDEDEELSPAAKEL
KKIKDELEDTQPIGSLIKLARTVDQAKALLTFVDAIAEKTLRNTVTLTAA
RGRGKSAAMGVAIAAAVAYGYSNIFITSPSPENLKTLFEFVFKGFDALDY
KDHADYTIIQSTNPEFNKAIVRVNIHRNHRQTIQYIRPQDAHVLGQAELV
VIDEAAAIPLPLVKKLMGPYLVFMASTISGYEGTGRSLSLKLIKQLREQS
RSLKEITLSEPIRYAQGDNVEKWLNTLLCLDPDPSQCELLHVNRDTLFSF
HPVSEKFLQQMVALYVASHYKNSPNDLQLMSDAPAHELFVLTGPIQEGRL
PEPLCVIQVSLEGKISKQSILKSLSRGQQPAGDLIPWLVSQQFQDDEFAS
LSGARIVRIATNPDYMSMGYGSKALQLLVDYYEGKFADIKVRDMHELPPL
FSKLSERRPEKLDYVGVSYGLTQQLHKFWKRAQFVPVYLRQTANDLTGEH
TCVMIRPLQDGNDPSWLGAFAADFHKRFLSLLSYKFREFPSILALTIEES
ANAGAMLDPSNAPTELTKAELDQLFTPFDHKRLESYANGLLDYHVVLDLM
PTIAQLYFTGRLREAVKLSGLQQAILLALGLQRKDIDTLATELNLPGSQV
LAIFMKIMRKVTQHFGALVSG

Ligand information

Ligand ID

A1AH4

InChI

InChI=1S/C32H49N10O22P3S/c1-32(2,12-60-67(57,58)64-66(55,56)59-10-16-24(63-65(52,53)54)23(48)30(62-16)42-14-38-20-26(33)36-13-37-27(20)42)25(49)28(50)35-5-3-18(44)34-6-8-68-11-19(45)39-17-4-7-41(31(51)40-17)29-22(47)21(46)15(9-43)61-29/h4,7,13-16,21-25,29-30,43,46-49H,3,5-6,8-12H2,1-2H3,(H,34,44)(H,35,50)(H,55,56)(H,57,58)(H2,33,36,37)(H2,52,53,54)(H,39,40,45,51)/t15-,16-,21+,22+,23+,24-,25+,29-,30-/m1/s1

InChIKey

CDGBUBJHIITENP-CLLAXTHFSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 2.0.7	CC(C)(COP(=O)(O)OP(=O)(O)OC[C@@H]1[C@H]([C@@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)[C@H](C(=O)NCCC(=O)NCCSCC(=O)NC4=NC(=O)N(C=C4)[C@H]5[C@H]([C@H]([C@H](O5)CO)O)O)O
ACDLabs 12.01	OC1C(O)C(CO)OC1N1C=CC(=NC1=O)NC(=O)CSCCNC(=O)CCNC(=O)C(O)C(C)(C)COP(=O)(O)OP(=O)(O)OCC1OC(n2cnc3c(N)ncnc32)C(O)C1OP(=O)(O)O
OpenEye OEToolkits 2.0.7	CC(C)(COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)C(C(=O)NCCC(=O)NCCSCC(=O)NC4=NC(=O)N(C=C4)C5C(C(C(O5)CO)O)O)O
CACTVS 3.385	CC(C)(CO[P](O)(=O)O[P](O)(=O)OC[C@H]1O[C@H]([C@@H](O)[C@@H]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[C@@H](O)C(=O)NCCC(=O)NCCSCC(=O)NC4=NC(=O)N(C=C4)[C@@H]5O[C@H](CO)[C@H](O)[C@@H]5O
CACTVS 3.385	CC(C)(CO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O[P](O)(O)=O)n2cnc3c(N)ncnc23)[CH](O)C(=O)NCCC(=O)NCCSCC(=O)NC4=NC(=O)N(C=C4)[CH]5O[CH](CO)[CH](O)[CH]5O

Formula

C32 H49 N10 O22 P3 S

Name

[[(2~{R},3~{S},4~{S},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(3~{R})-4-[[3-[2-[2-[[1-[(2~{R},3~{S},4~{R},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-2-oxidanylidene-pyrimidin-4-yl]amino]-2-oxidanylidene-ethyl]sulfanylethylamino]-3-oxidanylidene-propyl]amino]-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-butyl] hydrogen phosphate

ChEMBL

DrugBank

ZINC

PDB chain

9b0e Chain A Residue 1102 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	9b0e Molecular Basis for RNA Cytidine Acetylation by NAT10.
Resolution	3.19 Å
Binding residue (original residue number in PDB)	S547 H548 Y549 V636 I638 T640 M645 S646 M647 G648 G650 S651 V725 S726 Y727 Q732 L733 K735 F736 R739
Binding residue (residue number reindexed from 1)	S468 H469 Y470 V557 I559 T561 M566 S567 M568 G569 G571 S572 V617 S618 Y619 Q624 L625 K627 F628 R631
Annotation score	3

External links

PDB	RCSB:9b0e, PDBe:9b0e, PDBj:9b0e
PDBsum	9b0e
PubMed	38585770
UniProt	G0S273

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