6X9K: Human DNMT1(729-1600)

Human DNMT1(729-1600) Bound to Zebularine-Containing 12mer dsDNA and Inhibitor GSK3685032A. Determined by X-ray diffraction at 2.65 Å resolution. Released 7 Jul 2021.

Method
X-ray diffraction
Resolution
2.65 Å
Organism
Homo sapiens
Chains
3
Atoms
7,297
Mol. weight
107.26 kDa
Ligands
UXM, ZN
Released
7 Jul 2021

Explore 6X9K in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6X9K contains 55 α-helices and 58 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 55 helices, 58 β-strands

ElementResiduesLengthSheet
β-strand731-73331
β-strand739-74132
β-strand744-74742
β-strand749-75241
β-strand755-75841
β-strand762-76542
β-strand775-785112
β-strand789-799112
α-helix800-8023
α-helix806-8083
β-strand813-824122
α-helix825-8273
β-strand828-83252
β-strand834-83632
α-helix838-8403
α-helix843-8453
α-helix851-8555
β-strand863-87082
β-strand875-87732
α-helix878-8803
α-helix882-8854
α-helix894-90613
β-strand909-91023
β-strand913-91644
β-strand920-92344
β-strand925-92843
β-strand931-93443
β-strand938-94144
α-helix957-9593
α-helix970-9756
α-helix987-9893
β-strand992-1002114
β-strand100315
α-helix10041
β-strand100915
β-strand1015-102064
α-helix10211
β-strand102216
α-helix10231
α-helix1024-10263
α-helix1033-10364
β-strand1041-104447
β-strand1048-105254
α-helix1053-10553
β-strand1058-106034
β-strand1061-106447
α-helix1065-10673
α-helix1072-10765
β-strand1082-109097
β-strand1095-109737
α-helix1098-11003
α-helix1101-11033
α-helix1137-11382
β-strand1139-114462
α-helix1150-11578
β-strand1161-116772
α-helix1171-118010
β-strand1185-118732
α-helix1191-11999
β-strand120418
α-helix12091
β-strand121018
α-helix1211-12122
β-strand1219-122242
α-helix1234-12352
α-helix1237-12448
α-helix1247-125812
β-strand1262-126872
α-helix1269-12724
α-helix1274-129017
β-strand1293-130082
α-helix1301-13044
β-strand130819
β-strand1311-131882
α-helix1324-13307
β-strand1332110
α-helix1336-13383
β-strand1343-1345311
β-strand1348-1350311
β-strand1362110
α-helix1363-13653
α-helix1367-13715
α-helix1375-13762
β-strand1385-1386212
α-helix1395-14017
β-strand1409-1410212
α-helix1419-14268
α-helix1436-14383
β-strand1444-1445213
β-strand1451-1452213
β-strand1453114
β-strand1459115
β-strand1461116
β-strand1465116
β-strand1474115
α-helix1477-14793
α-helix1487-14893
β-strand1494114
α-helix1499-15035
α-helix1504-15063
α-helix1508-15103
α-helix15151
β-strand1516117
α-helix15171
β-strand152319
α-helix1524-15263
β-strand1540117
β-strand1547117
α-helix1548-15492
α-helix1550-15578
α-helix1569-157810
α-helix1580-15812
α-helix1582-159716

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
DNA (cytosine-5)-methyltransferase 1Aprotein874Homo sapiensP26358 (AlphaFold model)
DNA (5'-D(*GP*AP*GP*GP*CP*(5CM)P*GP*CP*CP*TP*GP*C)-3')CDNA12Homo sapiens
DNA (5'-d(*gp*cp*ap*gp*g)-r(p*(pyo))-d(p*gp*gp*cp*cp*tp*c)-3')DDNA12Homo sapiens
Sequence of entity 1 (A), FASTA
>6X9K_1 DNA (cytosine-5)-methyltransferase 1 (chains A)
HMNRISWVGEAVKTDGKKSYYKKVCIDAETLEVGDCVSVIPDDSSKPLYLARVTALWEDS
SNGQMFHAHWFCAGTDTVLGATSDPLELFLVDECEDMQLSYIHSKVKVIYKAPSENWAME
GGMDPESLLEGDDGKTYFYQLWYDQDYARFESPPKTQPTEDNKFKFCVSCARLAEMRQKE
IPRVLEQLEDLDSRVLYYSATKNGILYRVGDGVYLPPEAFTFNIKLSSPVKRPRKEPVDE
DLYPEHYRKYSDYIKGSNLDAPEPYRIGRIKEIFCPKKSNGRPNETDIKIRVNKFYRPEN
THKSTPASYHADINLLYWSDEEAVVDFKAVQGRCTVEYGEDLPECVQVYSMGGPNRFYFL
EAYNAKSKSFEDPPNHARSPGNKGKGKGKGKGKPKSQACEPSEPEIEIKLPKLRTLDVFS
GCGGLSEGFHQAGISDTLWAIEMWDPAAQAFRLNNPGSTVFTEDCNILLKLVMAGETTNS
RGQRLPQKGDVEMLCGGPPCQGFSGMNRFNSRTYSKFKNSLVVSFLSYCDYYRPRFFLLE
NVRNFVSFKRSMVLKLTLRCLVRMGYQCTFGVLQAGQYGVAQTRRRAIILAAAPGEKLPL
FPEPLHVFAPRACQLSVVVDDKKFVSNITRLSSGPFRTITVRDTMSDLPEVRNGASALEI
SYNGEPQSWFQRQLRGAQYQPILRDHICKDMSALVAARMRHIPLAPGSDWRDLPNIEVRL
SDGTMARKLRYTHHDRKNGRSSSGALRGVCSCVEAGKACDPAARQFNTLIPWCLPHTGNR
HNHWAGLYGRLEWDGFFSTTVTNPEPMGKQGRVLHPEQHRVVSVRECARSQGFPDTYRLF
GNILDKHRQVGNAVPPPLAKAIGLEIKLCMLAKA
Sequence of entity 2 (C), FASTA
>6X9K_2 DNA (5'-D(*GP*AP*GP*GP*CP*(5CM)P*GP*CP*CP*TP*GP*C)-3') (chains C)
GAGGCCGCCTGC
Sequence of entity 3 (D), FASTA
>6X9K_3 DNA (5'-D(*GP*CP*AP*GP*G)-R(P*(PYO))-D(P*GP*GP*CP*CP*TP*C)-3') (chains D)
GCAGGUGGCCTC

Ligands and cofactors

IDNameFormulaCopies
UXM(2R)-2-{[6-(4-aminopiperidin-1-yl)-3,5-dicyano-4-ethylpyridin-2-yl]sulfanyl}-2-…C22 H24 N6 O S1
ZNZinc ionZn2

Water and common crystallization additives (EDO) are not listed.

Primary citation

Discovery of a first-in-class reversible DNMT1-selective inhibitor with improved tolerability and efficacy in acute myeloid leukemia. Pappalardi, M.B., Keenan, K., Cockerill, M. et al. Nat Cancer (2021) 2:1002-1017. PubMed

Other PDB entries of the same protein (UniProt P26358 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

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