5UFI: DCN1

DCN1 bound to DI-591. Determined by X-ray diffraction at 2.58 Å resolution. Released 1 Nov 2017.

Method: X-ray diffraction
Resolution: 2.58 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,437
Mol. weight: 107.35 kDa
Ligands: 8B1
Released: 1 Nov 2017

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

Secondary structure: helices and β-sheets

5UFI contains 52 α-helices and 21 β-strands across 4 chains. 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: 13 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	62-70	9
β-strand	73-74	2	1
β-strand	77-81	5	1
α-helix	83-92	10
α-helix	100-108	9
β-strand	117-118	2	1
α-helix	119-129	11
α-helix	134-138	5
α-helix	141-147	7
α-helix	153-165	13
α-helix	167	1
β-strand	173-174	2	2
α-helix	175-185	11
α-helix	193-202	10
β-strand	207-208	2	2
α-helix	210-222	13
α-helix	238-247	10
α-helix	248-250	3

Chain B: 14 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	62-69	8
β-strand	73	1	3
β-strand	80-81	2	3
α-helix	83-92	10
α-helix	100-108	9
β-strand	117-118	2	3
α-helix	119-128	10
α-helix	134-147	14
α-helix	151-165	15
α-helix	167	1
β-strand	173	1	4
α-helix	175-185	11
α-helix	193-201	9
α-helix	206-207	2
β-strand	208	1	4
α-helix	209	1
α-helix	210-222	13
α-helix	238-247	10
α-helix	248-250	3

Chain C: 12 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	62-70	9
β-strand	73	1	5
β-strand	80	1	6
β-strand	81	1	5
α-helix	83-92	10
α-helix	100-108	9
β-strand	118	1	6
α-helix	119-129	11
α-helix	134-147	14
α-helix	153-165	13
α-helix	167	1
β-strand	173-174	2	7
α-helix	175-185	11
α-helix	193-203	11
β-strand	207-208	2	7
α-helix	210-222	13
α-helix	238-247	10
α-helix	248-250	3

Chain D: 13 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	62-72	11
β-strand	73	1	8
β-strand	80-81	2	8
α-helix	83-93	11
α-helix	100-108	9
β-strand	117-118	2	8
α-helix	119-129	11
α-helix	134-138	5
α-helix	141-147	7
α-helix	153-165	13
α-helix	167	1
β-strand	173-174	2	9
α-helix	175-185	11
α-helix	193-203	11
β-strand	207-208	2	9
α-helix	210-222	13
α-helix	238-247	10
α-helix	248-250	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DCN1-like protein 1	A, B, C, D	protein	225	Homo sapiens	Q96GG9 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>5UFI_1 DCN1-like protein 1 (chains A, B, C, D)
MSYYHHHHHHLESTSLYKKAGTMGSLDRKKLEQLYNRYKDPQDENKIGIDGIQQFCDDLA
LDPASISVLIIAWKFRAATQCEFSKQEFMDGMTELGCDSIEKLKAQIPKMEQELKEPGRF
KDFYQFTFNFAKNPGQKGLDLEMAIAYWNLVLNGRFKFLDLWNKFLLEHHKRSIPKDTWN
LLLDFSTMIADDMSNYDEEGAWPVLIDDFVEFARPQIAGTKSTTV

Ligands and cofactors

ID	Name	Formula	Copies
8B1	N-[(1S)-1-cyclohexyl-2-{[3-(morpholin-4-yl)propanoyl]amino}ethyl]-N~2~-propanoy…	C31 H47 N5 O4 S	4

Primary citation

A potent small-molecule inhibitor of the DCN1-UBC12 interaction that selectively blocks cullin 3 neddylation. Zhou, H., Lu, J., Liu, L. et al. Nat Commun (2017) 8:1150-1150. DOI 10.1038/s41467-017-01243-7 · PubMed

Other PDB entries of the same protein (UniProt Q96GG9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6BG3 1.05 Å, Structure of (3S,4S)-1-benzyl-4-(3-(3-(trifluoromethyl)phenyl)ureido)piperidin-3-yl…
6BG5 1.1 Å, Structure of 1-(benzo[d][1,3]dioxol-5-ylmethyl)-1-(1-propylpiperidin-4-yl)-3-(3-(trifluor…
5V86 1.37 Å, Structure of DCN1 bound to NAcM-OPT
6P5V 1.4 Å, Structure of DCN1 bound to N-((4S,5S)-7-ethyl-4-(4-fluorophenyl)-3-methyl-6-oxo-1-phenyl-…
3TDU 1.5 Å, N-terminal acetylation acts as an avidity enhancer within an interconnected multiprotein…
7KWA 1.57 Å, Structure of DCN1 bound to N-((4S,5S)-3-(aminomethyl)-7-ethyl-4-(4-fluorophenyl)-6-oxo-1-…
5V88 1.6 Å, Structure of DCN1 bound to NAcM-COV
6P5W 1.69 Å, Structure of DCN1 bound to 3-methyl-N-((4S,5S)-3-methyl-6-oxo-1-phenyl-4-(p-tolyl)-4,5,6,…
3TDZ 2.0 Å, N-terminal acetylation acts as an avidity enhancer within an interconnected multiprotein…
5V83 2.0 Å, Structure of DCN1 bound to NAcM-HIT
6XOO 2.06 Å, DCN1 bound to DI-1859
6XOP 2.07 Å, DCN1 bound to inhibitor 10

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