6P5W: DCN1

Structure of DCN1 bound to 3-methyl-N-((4S,5S)-3-methyl-6-oxo-1-phenyl-4-(p-tolyl)-4,5,6,7-tetrahydro-1H-pyrazolo[3,4-b]pyridin-5-yl)benzamide. Determined by X-ray diffraction at 1.69 Å resolution. Released 11 Sept 2019.

Method: X-ray diffraction
Resolution: 1.69 Å
Organisms: Enterobacteria phage T4, Homo sapiens
Chains: 1
Atoms: 3,323
Mol. weight: 44.76 kDa
Ligands: O0A
Released: 11 Sept 2019

Explore 6P5W in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6P5W contains 20 α-helices and 11 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: 20 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	-8--5	4
α-helix	3-10	8
β-strand	14-15	2	1
β-strand	16	1	2
β-strand	17-19	3	1
β-strand	25-28	4	1
β-strand	31-34	4	1
α-helix	39-50	12
β-strand	57	1	2
α-helix	60-79	20
α-helix	85-90	6
α-helix	93-112	20
α-helix	115-122	8
α-helix	126-134	9
α-helix	137-141	5
α-helix	143-155	13
α-helix	159-1072	17
β-strand	1073-1074	2	3
β-strand	1077-1081	5	3
α-helix	1083-1092	10
α-helix	1100-1108	9
β-strand	1117-1118	2	3
α-helix	1119-1128	10
α-helix	1134-1147	14
α-helix	1151-1165	15
β-strand	1173	1	4
α-helix	1175-1186	12
α-helix	1193-1202	10
β-strand	1208	1	4
α-helix	1210-1222	13
α-helix	1238-1255	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Lysozyme,DCN1-like protein 1 chimera	A	protein	384	Enterobacteria phage T4, Homo sapiens	D9IEF7, Q96GG9 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6P5W_1 Lysozyme,DCN1-like protein 1 chimera (chains A)
MGSSHHHHHHSQDLENLYFQGSMNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPS
LNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAA
LINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRTKRVITTFRTGTW
DAYKNLRKKLEQLYNRYKDPQDENKIGIDGIQQFCDDLALDPASISVLIIAWKFRAATQC
EFSKQEFMDGMTELGCDSIEKLKAQIPKMEQELKEPGRFKDFYQFTFNFAKNPGQKGLDL
EMAIAYWNLVLNGRFKFLDLWNKFLLEHHKRSIPKDTWNLLLDFSTMIADDMSNYDEEGA
WPVLIDDFVEFARPQIAGTKSTTV

Ligands and cofactors

ID	Name	Formula	Copies
O0A	3-methyl-N-[(4S,5S)-3-methyl-4-(4-methylphenyl)-6-oxo-1-phenyl-4,5,6,7-tetrahyd…	C28 H26 N4 O2	1

Primary citation

Discovery of Novel Pyrazolo-pyridone DCN1 Inhibitors Controlling Cullin Neddylation. Kim, H.S., Hammill, J.T., Scott, D.C. et al. J Med Chem (2019) 62:8429-8442. DOI 10.1021/acs.jmedchem.9b00410 · PubMed

Other PDB entries of the same protein (UniProt D9IEF7), best resolution first:

7LOG 0.99 Å, T4 lysozyme mutant L99A in complex with 3-butylpyridine
9DJK 1.04 Å, T4 Lysozyme D127H/V131H
7XE7 1.05 Å, T4 lysozyme mutant-S44C/C54T/N68C/A93C/C97A/T115C, pH10
7LXA 1.07 Å, T4 lysozyme mutant L99A
9DJM 1.08 Å, T4 Lysozyme K147H/T151H
7XE6 1.1 Å, T4 lysozyme mutant-S44C/C54T/N68C/A93C/C97A/T115C, pH7
7XEA 1.1 Å, T4 lysozyme mutant-S44C/C54T/N68C/A93C/C97A/T115C, DMSO 40%, and then backsoaking
9DJI 1.1 Å, T4 Lysozyme R119H/Q123H
9DJD 1.11 Å, T4 Lysozyme A73H/G77H/Y139F co-crystallized with Cu(II)-NTA
8F11 1.12 Å, T4 lysozyme with a 2,6-diazaadamantane nitroxide (DZD) spin label
9DJB 1.13 Å, T4 Lysozyme A73H/G77H
9DJC 1.13 Å, T4 Lysozyme A73H/G77H/Y139F

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