5V37: SMYD3 with SAM and EPZ028862

Crystal structure of SMYD3 with SAM and EPZ028862. Determined by X-ray diffraction at 1.42 Å resolution. Released 7 Mar 2018.

Method: X-ray diffraction
Resolution: 1.42 Å
Organism: Homo sapiens
Chains: 1
Atoms: 4,275
Mol. weight: 50.62 kDa
Ligands: ZN, SAM, 8WD
Released: 7 Mar 2018

Explore 5V37 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5V37 contains 27 α-helices and 18 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: 27 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	1
β-strand	16-20	5	1
β-strand	24	1	2
β-strand	29-33	5	3
β-strand	37-40	4	4
α-helix	42-44	3
β-strand	45	1	5
β-strand	48	1	5
β-strand	55	1	5
β-strand	60-61	2	6
α-helix	62	1
β-strand	69-70	2	6
α-helix	73-78	6
α-helix	80-93	14
α-helix	100-114	15
α-helix	116-118	3
α-helix	119-121	3
α-helix	126-128	3
α-helix	133-135	3
α-helix	138-154	17
α-helix	162-164	3
α-helix	166	1
α-helix	171-181	11
β-strand	183-186	4	4
β-strand	192-197	6	4
α-helix	201-203	3
α-helix	204	1
β-strand	205-206	2	7
β-strand	212-217	6	3
β-strand	220-225	6	3
β-strand	229	1	2
α-helix	233	1
β-strand	234	1	1
α-helix	235	1
β-strand	236-237	2	7
α-helix	246-255	10
α-helix	264-268	5
α-helix	272-275	4
α-helix	280-298	19
α-helix	302-313	12
α-helix	325-340	16
α-helix	344-361	18
α-helix	367-382	16
α-helix	386-403	18
α-helix	409-424	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone-lysine N-methyltransferase SMYD3	A	protein	428	Homo sapiens	Q9H7B4 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5V37_1 Histone-lysine N-methyltransferase SMYD3 (chains A)
MEPLKVEKFATANRGNGLRAVTPLRPGELLFRSDPLAYTVCKGSRGVVCDRCLLGKEKLM
RCSQCRVAKYCSAKCQKKAWPDHKRECKCLKSCKPRYPPDSVRLLGRVVFKLMDGAPSES
EKLYSFYDLESNINKLTEDKKEGLRQLVMTFQHFMREEIQDASQLPPAFDLFEAFAKVIC
NSFTICNAEMQEVGVGLYPSISLLNHSCDPNCSIVFNGPHLLLRAVRDIEVGEELTICYL
DMLMTSEERRKQLRDQYCFECDCFRCQTQDKDADMLTGDEQVWKEVQESLKKIEELKAHW
KWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTMEPYRI
FFPGSHPVRGVQVMKVGKLQLHQGMFPQAMKNLRLAFDIMRVTHGREHSLIEDLILLLEE
CDANIRAS

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	3
SAM	S-adenosylmethionine	C15 H22 N6 O5 S	1
8WD	N-{(3-endo)-8-[(trans-4-aminocyclohexyl)sulfonyl]-8-azabicyclo[3.2.1]octan-3-yl…	C20 H30 N4 O4 S	1

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

Primary citation

Small molecule inhibitors and CRISPR/Cas9 mutagenesis demonstrate that SMYD2 and SMYD3 activity are dispensable for autonomous cancer cell proliferation. Thomenius, M.J., Totman, J., Harvey, D. et al. PLoS One (2018) 13:e0197372-e0197372. DOI 10.1371/journal.pone.0197372 · PubMed

Other PDB entries of the same protein (UniProt Q9H7B4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6P7Z 1.19 Å, Co-crystal Structure of human SMYD3 with Isoxazole Amides Inhibitors
6PAF 1.24 Å, Co-crystal Structure of human SMYD3 with Isoxazole Amides Inhibitors
5CCL 1.5 Å, Crystal structure of SMYD3 with SAM and oxindole compound
7O2C 1.52 Å, X-RAY STRUCTURE OF SMYD3 IN COMPLEX WITH the benzodiazepine-based probe BAY-6035
3QWP 1.53 Å, Crystal structure of SET and MYND domain containing 3; Zinc finger MYND…
6P6K 1.55 Å, Co-crystal Structure of human SMYD3 with Isoxazole Amides Inhibitors
6ZRB 1.55 Å, Crystal structure of SMYD3 conjugate with piperidine-based covalent inhibitor EM127
7O2A 1.57 Å, X-RAY STRUCTURE OF SMYD3 IN COMPLEX WITH benzodiazepine-type inhibitor compound 15
7QNR 1.57 Å, SMYD3 in complex with fragment FL01791
6O9O 1.59 Å, Crystal Structure of SMYD3 with Potent and Selective Isoxazole Amide Inhibitor 1
6P6G 1.59 Å, Co-crystal Structure of human SMYD3 with Isoxazole Amides Inhibitors
7BJ1 1.61 Å, Crystal structure of SMYD3 with diperodon S enantiomer bound to allosteric site

Browse structure collections

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