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- PDB-4hyf: Structural basis and SAR for OD 270, a lead stage 1,2,4-triazole ... -

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Basic information

Entry
Database: PDB / ID: 4hyf
TitleStructural basis and SAR for OD 270, a lead stage 1,2,4-triazole based specific Tankyrase1/2 inhibitor
ComponentsTankyrase-2
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / CATALYTIC FRAGMENT / PARP / ADP-RIBOSYLATION / ANK REPEAT / CHROMOSOMAL PROTEIN / GLYCOSYLTRANSFERASE / PHOSPHORYLATION / TELOMERE / TRANSFERASE / TRANSLOCATION / TRANSPORT / WNT-SIGNALLING / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


XAV939 stabilizes AXIN / NAD+ ADP-ribosyltransferase / protein localization to chromosome, telomeric region / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / protein poly-ADP-ribosylation / pericentriolar material / NAD+-protein ADP-ribosyltransferase activity / positive regulation of telomere capping / NAD+ ADP-ribosyltransferase activity ...XAV939 stabilizes AXIN / NAD+ ADP-ribosyltransferase / protein localization to chromosome, telomeric region / negative regulation of telomere maintenance via telomere lengthening / protein auto-ADP-ribosylation / protein poly-ADP-ribosylation / pericentriolar material / NAD+-protein ADP-ribosyltransferase activity / positive regulation of telomere capping / NAD+ ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / positive regulation of telomere maintenance via telomerase / nucleotidyltransferase activity / TCF dependent signaling in response to WNT / Degradation of AXIN / Wnt signaling pathway / Regulation of PTEN stability and activity / protein polyubiquitination / positive regulation of canonical Wnt signaling pathway / nuclear envelope / chromosome, telomeric region / Ub-specific processing proteases / Golgi membrane / perinuclear region of cytoplasm / enzyme binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ankyrin repeat / Phosphoenolpyruvate Carboxykinase; domain 3 - #10 / Phosphoenolpyruvate Carboxykinase; domain 3 / Ankyrin repeats (many copies) / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. ...Ankyrin repeat / Phosphoenolpyruvate Carboxykinase; domain 3 - #10 / Phosphoenolpyruvate Carboxykinase; domain 3 / Ankyrin repeats (many copies) / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile. / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-1AK / NICOTINAMIDE / Poly [ADP-ribose] polymerase tankyrase-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsPerdreau, H. / Ekblad, B. / Voronkov, A. / Holsworth, D.D. / Waaler, J. / Drewes, G. / Schueler, H. / Krauss, S. / Morth, J.P.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Structural Basis and SAR for G007-LK, a Lead Stage 1,2,4-Triazole Based Specific Tankyrase 1/2 Inhibitor.
Authors: Voronkov, A. / Holsworth, D.D. / Waaler, J. / Wilson, S.R. / Ekblad, B. / Perdreau-Dahl, H. / Dinh, H. / Drewes, G. / Hopf, C. / Morth, J.P. / Krauss, S.
History
DepositionNov 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1May 1, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tankyrase-2
B: Tankyrase-2
C: Tankyrase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,05212
Polymers81,8993
Non-polymers2,1529
Water59433
1
A: Tankyrase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0174
Polymers27,3001
Non-polymers7173
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tankyrase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0174
Polymers27,3001
Non-polymers7173
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Tankyrase-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0174
Polymers27,3001
Non-polymers7173
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)151.540, 151.540, 140.520
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Tankyrase-2 / / TANK2 / ADP-ribosyltransferase diphtheria toxin-like 6 / ARTD6 / Poly [ADP-ribose] polymerase 5B / ...TANK2 / ADP-ribosyltransferase diphtheria toxin-like 6 / ARTD6 / Poly [ADP-ribose] polymerase 5B / TNKS-2 / TRF1-interacting ankyrin-related ADP-ribose polymerase 2 / Tankyrase II / Tankyrase-like protein / Tankyrase-related protein


Mass: 27299.764 Da / Num. of mol.: 3 / Fragment: Catalytic domain, UNP residues 946-1162
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARP5B, TANK2, TNKL, TNKS2 / Plasmid: PNIC-BSA4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rosetta II / References: UniProt: Q9H2K2, NAD+ ADP-ribosyltransferase
#2: Chemical ChemComp-NCA / NICOTINAMIDE / Nicotinamide


Mass: 122.125 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H6N2O / Comment: medication*YM
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-1AK / 4-{5-[(E)-2-{4-(2-chlorophenyl)-5-[5-(methylsulfonyl)pyridin-2-yl]-4H-1,2,4-triazol-3-yl}ethenyl]-1,3,4-oxadiazol-2-yl}benzonitrile


Mass: 529.958 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C25H16ClN7O3S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O

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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: 5.69 Å3/Da / Density % sol: 78.37 %
Crystal growTemperature: 310 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 100 mM NaOAc pH 4.5 and 16-26% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 310K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.28243 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28243 Å / Relative weight: 1
ReflectionResolution: 2.8→45 Å / Num. all: 177646 / Num. obs: 175910 / % possible obs: 99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.8-2.87198
2.87-2.95199.6
2.95-3.04199.6
3.04-3.47199.3
3.47-5.11199
5.11-7.23199

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Processing

Software
NameVersionClassification
RemDAqdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
PROCESSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MHJ

3mhj


Resolution: 2.8→24.858 Å / SU ML: 0.37 / σ(F): 1.2 / Phase error: 25.13 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2254 4489 5.07 %Random
Rwork0.2114 ---
all0.2121 88723 --
obs0.212 88591 99.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→24.858 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5433 0 141 33 5607
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045733
X-RAY DIFFRACTIONf_angle_d0.6767725
X-RAY DIFFRACTIONf_dihedral_angle_d14.5652139
X-RAY DIFFRACTIONf_chiral_restr0.055753
X-RAY DIFFRACTIONf_plane_restr0.0031011
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8002-2.8320.39921340.36332737X-RAY DIFFRACTION97
2.832-2.86530.32171400.3492793X-RAY DIFFRACTION100
2.8653-2.90010.36811430.34422775X-RAY DIFFRACTION100
2.9001-2.93680.30671480.33552820X-RAY DIFFRACTION100
2.9368-2.97540.38051700.31792834X-RAY DIFFRACTION100
2.9754-3.01610.34131580.32572768X-RAY DIFFRACTION100
3.0161-3.05910.36031620.30262772X-RAY DIFFRACTION100
3.0591-3.10470.32841390.29542812X-RAY DIFFRACTION100
3.1047-3.15310.30261510.28912837X-RAY DIFFRACTION100
3.1531-3.20470.2911440.27462798X-RAY DIFFRACTION100
3.2047-3.25980.27571760.27122790X-RAY DIFFRACTION100
3.2598-3.3190.29211360.25382823X-RAY DIFFRACTION100
3.319-3.38260.29221320.2432815X-RAY DIFFRACTION100
3.3826-3.45150.27021430.242860X-RAY DIFFRACTION100
3.4515-3.52640.26191630.23122756X-RAY DIFFRACTION100
3.5264-3.60810.24581640.23242768X-RAY DIFFRACTION100
3.6081-3.69810.25231400.22432850X-RAY DIFFRACTION100
3.6981-3.79770.22141420.20432835X-RAY DIFFRACTION100
3.7977-3.90910.17191670.18832753X-RAY DIFFRACTION100
3.9091-4.03480.20431600.192801X-RAY DIFFRACTION100
4.0348-4.17830.2111270.17582818X-RAY DIFFRACTION100
4.1783-4.34480.16871410.16222811X-RAY DIFFRACTION100
4.3448-4.54140.13781350.14912819X-RAY DIFFRACTION100
4.5414-4.77920.151870.14552793X-RAY DIFFRACTION100
4.7792-5.07620.1671290.15062841X-RAY DIFFRACTION100
5.0762-5.46430.18311330.15832815X-RAY DIFFRACTION100
5.4643-6.00720.17291880.1682758X-RAY DIFFRACTION100
6.0072-6.86040.2161360.18582833X-RAY DIFFRACTION100
6.8604-8.58390.17641540.16842803X-RAY DIFFRACTION100
8.5839-24.85930.17961470.17522814X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2983-0.20560.04790.5442-0.39030.33660.2440.36060.2362-0.1939-0.07370.0448-0.03010.07830.00010.5679-0.0071-0.00520.8661-0.06140.6217-24.434159.843912.4709
20.08150.0591-0.08250.0675-0.05520.0695-0.13760.01860.03320.2399-0.3959-0.4246-0.093-0.3918-0.00010.63210.06290.06320.73-0.04250.8304-13.035445.62831.8851
31.04950.1114-0.07940.3081-0.18440.68740.01070.1834-0.0416-0.0594-0.1295-0.18950.05660.1027-00.6401-0.0130.06050.8689-0.03730.7556-5.086457.692218.3239
40.08270.0214-0.0220.12910.00210.1597-0.0364-0.1350.07690.5596-0.05110.53750.2047-0.111900.7032-0.05740.0490.8703-0.05420.9656-26.638651.797629.337
50.28020.07790.09990.22870.1110.06160.08340.39140.50980.0114-0.02470.0752-0.15160.0604-0.00010.5526-0.04480.0430.60920.08510.6228-34.571777.437424.8427
60.28250.18370.45131.02490.07550.75230.01660.257-0.7072-0.331-0.1973-0.41330.54810.00460.00730.2761-0.04710.11880.3833-0.16590.424-45.11664.083745.5267
71.08240.36570.1710.695-0.40040.5930.09780.28990.1435-0.09030.00240.1236-0.1876-0.241800.61930.0284-0.00770.81460.01980.6916-53.669972.480829.5351
80.10010.00370.14110.0636-0.06080.25490.20320.5285-0.67290.0680.0454-0.32280.2890.3889-00.6263-0.00320.01660.79180.01980.8059-31.830464.706538.2697
90.1681-0.12270.13340.1111-0.09280.24320.00210.1169-0.3271-0.1884-0.363-0.62440.51780.5212-00.90010.18920.1430.8399-0.04591.2133-7.63922.304835.8948
100.0385-0.20990.11.0714-0.51980.25120.0478-0.33420.1290.09490.1810.56090.2392-0.5380.16490.1464-0.04040.04480.389-0.08660.3436-25.226740.526127.0261
110.87360.00350.16680.5747-0.01110.808-0.01580.3102-0.3727-0.47530.0619-0.1041.02490.0174-01.1785-0.04210.06090.6729-0.18890.9269-22.924521.254622.4227
120.1161-0.0143-0.09550.01330.01950.1230.241-0.586-0.0350.5402-0.2510.08220.1077-0.0539-00.85160.0287-0.00110.87380.02911.0958-17.061938.14439.9238
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 1046:1064 OR RESID 1103:1144 ) )A1046 - 1064
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 1046:1064 OR RESID 1103:1144 ) )A1103 - 1144
3X-RAY DIFFRACTION2( CHAIN A AND RESID 936:951 )A936 - 951
4X-RAY DIFFRACTION3( CHAIN A AND ( RESID 952:1002 OR RESID 1027:1045 OR RESID 1065:1102 OR RESID 1145:1162 ) )A952 - 1002
5X-RAY DIFFRACTION3( CHAIN A AND ( RESID 952:1002 OR RESID 1027:1045 OR RESID 1065:1102 OR RESID 1145:1162 ) )A1027 - 1045
6X-RAY DIFFRACTION3( CHAIN A AND ( RESID 952:1002 OR RESID 1027:1045 OR RESID 1065:1102 OR RESID 1145:1162 ) )A1065 - 1102
7X-RAY DIFFRACTION3( CHAIN A AND ( RESID 952:1002 OR RESID 1027:1045 OR RESID 1065:1102 OR RESID 1145:1162 ) )A1145 - 1162
8X-RAY DIFFRACTION4( CHAIN A AND RESID 1003:1026 )A1003 - 1026
9X-RAY DIFFRACTION5( CHAIN B AND ( RESID 1046:1064 OR RESID 1103:1144 ) )B1046 - 1064
10X-RAY DIFFRACTION5( CHAIN B AND ( RESID 1046:1064 OR RESID 1103:1144 ) )B1103 - 1144
11X-RAY DIFFRACTION6( CHAIN B AND RESID 936:951 )B936 - 951
12X-RAY DIFFRACTION7( CHAIN B AND ( RESID 952:1002 OR RESID 1027:1045 OR RESID 1065:1102 OR RESID 1145:1162 ) )B952 - 1002
13X-RAY DIFFRACTION7( CHAIN B AND ( RESID 952:1002 OR RESID 1027:1045 OR RESID 1065:1102 OR RESID 1145:1162 ) )B1027 - 1045
14X-RAY DIFFRACTION7( CHAIN B AND ( RESID 952:1002 OR RESID 1027:1045 OR RESID 1065:1102 OR RESID 1145:1162 ) )B1065 - 1102
15X-RAY DIFFRACTION7( CHAIN B AND ( RESID 952:1002 OR RESID 1027:1045 OR RESID 1065:1102 OR RESID 1145:1162 ) )B1145 - 1162
16X-RAY DIFFRACTION8( CHAIN B AND RESID 1003:1026 )B1003 - 1026
17X-RAY DIFFRACTION9( CHAIN C AND ( RESID 1046:1064 OR RESID 1103:1144 ) )C1046 - 1064
18X-RAY DIFFRACTION9( CHAIN C AND ( RESID 1046:1064 OR RESID 1103:1144 ) )C1103 - 1144
19X-RAY DIFFRACTION10( CHAIN C AND RESID 936:951 )C936 - 951
20X-RAY DIFFRACTION11( CHAIN C AND ( RESID 952:1002 OR RESID 1027:1045 OR RESID 1065:1102 OR RESID 1145:1162 ) )C952 - 1002
21X-RAY DIFFRACTION11( CHAIN C AND ( RESID 952:1002 OR RESID 1027:1045 OR RESID 1065:1102 OR RESID 1145:1162 ) )C1027 - 1045
22X-RAY DIFFRACTION11( CHAIN C AND ( RESID 952:1002 OR RESID 1027:1045 OR RESID 1065:1102 OR RESID 1145:1162 ) )C1065 - 1102
23X-RAY DIFFRACTION11( CHAIN C AND ( RESID 952:1002 OR RESID 1027:1045 OR RESID 1065:1102 OR RESID 1145:1162 ) )C1145 - 1162
24X-RAY DIFFRACTION12( CHAIN C AND RESID 1003:1026 )C1003 - 1026

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