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- PDB-7bn8: Notum fragment_3 (4H,5H-naphtho[1,2-b]thiophene-2-carboxylic acid) -

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Basic information

Entry
Database: PDB / ID: 7bn8
TitleNotum fragment_3 (4H,5H-naphtho[1,2-b]thiophene-2-carboxylic acid)
ComponentsPalmitoleoyl-protein carboxylesterase NOTUM
KeywordsHYDROLASE / Notum Inhibitor
Function / homology
Function and homology information


[Wnt protein] O-palmitoleoyl-L-serine hydrolase / protein depalmitoleylation / palmitoleyl hydrolase activity / phospholipase C activity / Release of Hh-Np from the secreting cell / regulation of bone mineralization / negative regulation of Wnt signaling pathway / Post-translational protein phosphorylation / bone development / negative regulation of canonical Wnt signaling pathway ...[Wnt protein] O-palmitoleoyl-L-serine hydrolase / protein depalmitoleylation / palmitoleyl hydrolase activity / phospholipase C activity / Release of Hh-Np from the secreting cell / regulation of bone mineralization / negative regulation of Wnt signaling pathway / Post-translational protein phosphorylation / bone development / negative regulation of canonical Wnt signaling pathway / Wnt signaling pathway / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / endoplasmic reticulum lumen / extracellular region
Similarity search - Function
Pectinacetylesterase/NOTUM / Pectinacetylesterase
Similarity search - Domain/homology
4H,5H-naphtho[1,2-b]thiophene-2-carboxylic acid / Palmitoleoyl-protein carboxylesterase NOTUM
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsZhao, Y. / Jones, E.Y.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UKC375/A17721 United Kingdom
CitationJournal: To Be Published
Title: Notum Inhibitor
Authors: Zhao, Y. / Jones, E.Y.
History
DepositionJan 21, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Palmitoleoyl-protein carboxylesterase NOTUM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4037
Polymers43,5671
Non-polymers8366
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint-43 kcal/mol
Surface area15250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.440, 72.426, 79.347
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Palmitoleoyl-protein carboxylesterase NOTUM / hNOTUM


Mass: 43567.148 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NOTUM, OK/SW-CL.30 / Production host: Homo sapiens (human)
References: UniProt: Q6P988, [Wnt protein] O-palmitoleoyl-L-serine hydrolase
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-U4T / 4H,5H-naphtho[1,2-b]thiophene-2-carboxylic acid / 4,5-Dihydronaphtho[1,2-b]thiophene-2-carboxylic acid / 4,5-dihydrobenzo[g][1]benzothiole-2-carboxylic acid


Mass: 230.282 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C13H10O2S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 38.29 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop
Details: 1.5 M Ammonium Sulphate 0.1 M Sodium Citrate, pH4.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 1.78→72.43 Å / Num. obs: 34091 / % possible obs: 99.5 % / Redundancy: 12.7 % / CC1/2: 0.998 / Net I/σ(I): 10.3
Reflection shellResolution: 1.78→1.81 Å / Num. unique obs: 1453 / CC1/2: 0.678

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
xia2data scaling
PDB_EXTRACT3.27data extraction
xia2data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4uz1

4uz1


Resolution: 1.78→53.49 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2325 1590 4.72 %
Rwork0.2003 32095 -
obs0.2018 33685 98.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.39 Å2 / Biso mean: 28.6214 Å2 / Biso min: 14.46 Å2
Refinement stepCycle: final / Resolution: 1.78→53.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2727 0 50 75 2852
Biso mean--44.92 31.36 -
Num. residues----348
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.78-1.830.3921350.32812610274590
1.83-1.90.32461340.29232882301698
1.9-1.980.30521390.25852867300698
1.98-2.070.29411640.23112874303898
2.07-2.170.25771290.21582902303199
2.17-2.310.22111390.19152925306499
2.31-2.490.23171570.18842934309199
2.49-2.740.24061500.197529543104100
2.74-3.140.23741520.193929703122100
3.14-3.950.2111400.176630263166100
3.95-53.490.18951510.18631513302100
Refinement TLS params.Method: refined / Origin x: 4.6271 Å / Origin y: -1.3182 Å / Origin z: -2.381 Å
111213212223313233
T0.1549 Å2-0.0035 Å2-0.0023 Å2-0.1943 Å20.0248 Å2--0.1604 Å2
L1.0431 °20.2354 °2-0.1511 °2-1.3712 °20.1218 °2--0.7315 °2
S-0.0231 Å °0.0718 Å °0.0404 Å °-0.0189 Å °0.0137 Å °0.014 Å °-0.0915 Å °-0.0265 Å °0.0117 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA88 - 929
2X-RAY DIFFRACTION1allB1

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