Structure of PDB 6x9i Chain A

Receptor sequence

>6x9iA (length=815) Species: 9606 (Homo sapiens) [Search protein sequence]

RISWVGEAVKTDGKKSYYKKVCIDAETLEVGDCVSVIPDDSSKPLYLARV
TALWEDSSNGQMFHAHWFCAGTDTVLGATSDPLELFLVDECEDMQLSYIH
SKVKVIYKAPSENWAMEGGMDKTYFYQLWYDQDYARFESPPKTQPNKFKF
CVSCARLAEMRQKEIPRVLEQLEDLDSRVLYYSATKNGILYRVGDGVYLP
PEAFTFNIPVDEDLYPEHYRKYSDYIKGSNLDAPEPYRIGRIKEIFCPKK
SNGRPNETDIKIRVNKFYRPENTHKSTPASYHADINLLYWSDEEAVVDFK
AVQGRCTVEYGEDLPECVQVYSMGGPNRFYFLEAYNAKSKSFEDPPNHAR
LPKLRTLDVFSGCGGLSEGFHQAGISDTLWAIEMWDPAAQAFRLNNPGST
VFTEDCNILLKLVMAGETTNSRGQRLPQKGDVEMLCGGPPCQGFSGMNRF
NSRTYSKFKNSLVVSFLSYCDYYRPRFFLLENVRNFVSFKRSMVLKLTLR
CLVRMGYQCTFGVLQAGQYGVAQTRRRAIILAAAPGEKLPLFPEPLHVFA
PRACQLSVVVDDKKFVSNITRLSSGPFRTITVRDTMSDLPEVRNGASALE
ISYNGEPQSWFQRQLRGAQYQPILRDHICKDMSALVAARMRHIPLAPGSD
WRDLPNIEVRLSDGTMARKLRYTHHDRKNGRSSSGALRGVCSCVEAGKAC
DPAARQFNTLIPWCLPHTGNRHNHWAGLYGRLEWDGFFSTTVTNPEPMGK
QGRVLHPEQHRVVSVRECARSQGFPDTYRLFGNILDKHRQVGNAVPPPLA
KAIGLEIKLCMLAKA

3D structure

PDB

6x9i Discovery of a first-in-class reversible DNMT1-selective inhibitor with improved tolerability and efficacy in acute myeloid leukemia.

Chain

Resolution

2.2 Å

3D
structure

Catalytic site residues are labeled in the structure
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Enzymatic activity

Catalytic site (original residue number in PDB)	C1226 E1266 R1310 R1312
Catalytic site (residue number reindexed from 1)	C441 E481 R525 R527
Enzyme Commision number	2.1.1.37: DNA (cytosine-5-)-methyltransferase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	dna	A	G1231 R1234 R1269 R1490 C1499 H1502 R1506 H1507 W1510 M1533 K1535	G446 R449 R484 R705 C714 H717 R721 H722 W725 M748 K750
BS02	dna	A	Y976 S977 Y979 K981 C1226 Q1227 S1230 G1231 M1232 N1233 F1235 V1268 R1312 N1508 V1527 T1528 G1534 K1535 G1577 N1578	Y222 S223 Y225 K227 C441 Q442 S445 G446 M447 N448 F450 V483 R527 N723 V742 T743 G749 K750 G792 N793
BS03	SAH	A	F1145 S1146 G1150 E1168 M1169 D1190 C1191 G1223 N1578 A1579	F360 S361 G365 E383 M384 D405 C406 G438 N793 A794	BindingDB: IC50=4000nM
BS04	ZN	A	C1476 C1478 C1485 H1502	C691 C693 C700 H717
BS05	ZN	A	H793 C820 C893 C896	H64 C91 C151 C154

Gene Ontology

	Molecular Function
GO:0003682	chromatin binding
GO:0008168	methyltransferase activity

View graph for
Molecular Function

External links

PDB	RCSB:6x9i, PDBe:6x9i, PDBj:6x9i
PDBsum	6x9i
PubMed	34790902
UniProt	P26358\|DNMT1_HUMAN DNA (cytosine-5)-methyltransferase 1 (Gene Name=DNMT1)

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