5CCL: SMYD3 with SAM and oxindole compound

Crystal structure of SMYD3 with SAM and oxindole compound. Determined by X-ray diffraction at 1.5 Å resolution. Released 9 Sept 2015.

Method: X-ray diffraction
Resolution: 1.5 Å
Organism: Homo sapiens
Chains: 1
Atoms: 4,170
Mol. weight: 50.85 kDa
Ligands: ZN, SAM, 4ZW
Released: 9 Sept 2015

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

Secondary structure: helices and β-sheets

5CCL contains 26 α-helices and 17 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: 26 helices, 17 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	48	1	5
β-strand	55	1	5
β-strand	60-61	2	6
β-strand	69-70	2	6
α-helix	73-93	21
α-helix	100-114	15
α-helix	116-117	2
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
α-helix	182	1
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	246-257	12
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	409-425	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone-lysine N-methyltransferase SMYD3	A	protein	432	Homo sapiens	Q9H7B4 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5CCL_1 Histone-lysine N-methyltransferase SMYD3 (chains A)
MEPLKVEKFATANRGNGLRAVTPLRPGELLFRSDPLAYTVCKGSRGVVCDRCLLGKEKLM
RCSQCRVAKYCSAKCQKKAWPDHKRECKCLKSCKPRYPPDSVRLLGRVVFKLMDGAPSES
EKLYSFYDLESNINKLTEDKKEGLRQLVMTFQHFMREEIQDASQLPPAFDLFEAFAKVIC
NSFTICNAEMQEVGVGLYPSISLLNHSCDPNCSIVFNGPHLLLRAVRDIEVGEELTICYL
DMLMTSEERRKQLRDQYCFECDCFRCQTQDKDADMLTGDEQVWKEVQESLKKIEELKAHW
KWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTMEPYRI
FFPGSHPVRGVQVMKVGKLQLHQGMFPQAMKNLRLAFDIMRVTHGREHSLIEDLILLLEE
CDANIRASFULL

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	3
SAM	S-adenosylmethionine	C15 H22 N6 O5 S	1
4ZW	2-oxidanylidene-N-piperidin-4-yl-1,3-dihydroindole-5-carboxamide	C14 H17 N3 O2	2

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

Primary citation

Novel Oxindole Sulfonamides and Sulfamides: EPZ031686, the First Orally Bioavailable Small Molecule SMYD3 Inhibitor. Mitchell, L.H., Boriack-Sjodin, P.A., Smith, S. et al. ACS Med Chem Lett (2016) 7:134-138. DOI 10.1021/acsmedchemlett.5b00272 · 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
5V37 1.42 Å, Crystal structure of SMYD3 with SAM and EPZ028862
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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