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PDB ID Mentions in PubMed Central Article count: 5

Citations in PubMed

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PDB ID Mentions in PubMed Central

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Structural and evolutionary classification of Type II restriction enzymes based on theoretical and experimental analyses.

(2008) Nucleic Acids Res 36

PubMed: 18456708 | PubMedCentral: PMC2441816 | DOI: 10.1093/nar/gkn175

to be published (PDB 3brv) P 4 BcgI 31 Mutagenesis BcgI ( 103 ) C 3 TaqI 6 Mutagenesis TaqI ( 104 ) P 3 HindIII 11 Mutagenesis HindIII ( 105 ) P 3 Eco57I 37 Mutagenesis Eco57I ( 106 ) C 3 MboI 40 Muta... enesis MboI ( 43 ) P 3 Bsp6I 15 Mutagenesis Bsp6I ( 47 ) P 3 NlaIV 10 Mutagenesis, CD NlaIV ( 46 ) P 3 Mva1269I 3 Mutagenesis Mva1269I ( 45 ) S 3 HpaI 1 Mutagenesis HpaI ( 48 ) P 3 BpuJI 73 Mutagenesis BpuJI ( 107 ) S 3 BtsIA 1 Mutagenesis BtsIA ( 108 ) S 3 BtsIB 1 Mutagenesis BtsIB ( 108 ) S 3 R2.BsrDI 3 Mutagenesis R2.BsrDI ( 108 ) S 3 R1.BsrDI 2 Mutagenesis R1.BsrDI ( 108 ) S 3 NgoPII 21 Mutagenesis NgoPII J.M.B. and coworkers, unpublished data P 3 XbaI 15 Sequence analysis ( 109 ) P 2 SalI 15 Sequence analysis ( 109 ) P 2 XmaI 9 Sequence analysis ( 110 ) E,P 2 Bpu10IB 18 Sequence analysis ( 111 ) S,P 2 DdeI 5 Sequence analysis ( 111 ) P 2 PvuRts1 46 Sequence analysis ( 22 , 34 ) ?

Publication Year: 2008


Inhibition of the NEMO/IKK? association complex formation, a novel mechanism associated with the NF-?B activation suppression by Withania somnifera's key metabolite withaferin A.

(2010) BMC Genomics 11 Suppl 4

PubMed: 21143809 | PubMedCentral: PMC3005936 | DOI: 10.1186/1471-2164-11-S4-S25

Structural aspects of NEMO/IKKβ association domain The structural features of the receptor macromolecule [PDB: 3BRV] have been described in detail elsewhere [ 25 ] by the depositors of the cry... tal structure to the Protein Data Bank.

Methods Ligand and receptors The crystal structure of the NEMO/IKKβ association domain [PDB: 3BRV] was obtained from the Protein Data Bank (PDB) [ 26 ].

Publication Year: 2010


Identification of human IKK-2 inhibitors of natural origin (part I): modeling of the IKK-2 kinase domain, virtual screening and activity assays.

(2011) PLoS One 6

PubMed: 21390216 | PubMedCentral: PMC3044726 | DOI: 10.1371/journal.pone.0016903

At present, there are only two entries in the Protein Data Bank ( http://www.pdb.org ; PDB) [38] for hIKK-2 ( i.e. , PDB codes 3BRT and 3BRV), and in both cases, they correspond to the... NEMO-binding region located at the C-terminal end of the protein [39] (therefore, no experimental structure for the kinase domain of hIKK-2 is known).

Publication Year: 2011


Highly precise protein-protein interaction prediction based on consensus between template-based and de novo docking methods.

(2013) BMC Proc 7

PubMed: 24564962 | PubMedCentral: PMC4044902 | DOI: 10.1186/1753-6561-7-S7-S6

Table 1 Protein and PDB ID list of human apoptosis pathway dataset Protein Name PDB ID (_Chain) AIF 1M6I _A AKT1 1UNQ _A 3CQW _A 3O96 _A AKT2 1MRV _A 1O6K _A 1O6L _A 1P6S _A AKT3 2X18 _A APAF1 1CY5 _A... 1Z6T _A 2YGS _A 3IZA _A 3YGS _C BCL-2 2W3L _A 2XA0 _A BCL-XL 2B48 _A 3FDL _A BID 2BID _A 2KBW _B Bax 1F16 _A 2G5B _I 2XA0 _C 3PK1 _B CASP3 1RHQ _A 1RHQ _B 2DKO _A 2DKO _B 2J32 _A CASP6 2WDP _A CASP7 1F1J _A 1I4O _A 1I51 _A 1I51 _B 2QL9 _A 2QL9 _B CASP8 1QTN _A 1QTN _B 2FUN _B 3H11 _B CASP9 1JXQ _A 1NW9 _B 3D9T _C 3YGS _P Calpain1 1ZCM _A Calpain2 1KFU _L 2NQA _A Cn(CHP) 2E30 _A Cn(CHP2) 2BEC _A Cn(PPP3CA) 1AUI _A 1MF8 _A 2R28 _C 3LL8 _A Cn(PPP3R1) 1AUI _B 1MF8 _B 3LL8 _B CytC 1J3S _A DFF40 1IBX _A DFF45 1IBX _B 1IYR _A FADD 1A1W _A 2GF5 _A 3EZQ _B FLIP 3H11 _A Fas 3EWT _E 3EZQ _A IAP(BIRC2) 3D9T _A 3M1D _A 3MUP _A IAP(BIRC3) 2UVL _A 3EB5 _A 3EB6 _A 3M0A _D 3M0D _D IAP(BIRC4) 1G73 _C 1I4O _C 1I51 _E 1NW9 _A 2ECG _A 2KNA _A 2POI _A 3CM7 _C IκBα 1IKN _D 1NFI _E IKK 2JVX _A 3BRT _B 3BRV _B 3CL3 _D 3FX0 _A IL-1(A) 2ILA _A IL-1(B) 1ITB _A 2NVH _A 3O4O _A IL-1R(1) 1ITB _B IL-1R(RAP) 3O4O _B IL-3 1JLI _A IL-3R 1EGJ _A IRAK2 3MOP _K IRAK4 2NRU _A 3MOP _G MyD88 2JS7 _A 3MOP _A NF-κB(NFKB1) 1IKN _C 1NFI _B 1SVC _P 2DBF _A NF-κB(RELA) 1IKN _A 1NFI _A NGF 1WWW _V 2IFG _E PI3K(PIK3CA) 2ENQ _A 2V1Y _A 3HHM _A PI3K(PIK3CG) 1E8Y _A PI3K(PIK3R1) 1A0N _A 1H9O _A 1PBW _A 2IUG _A 2V1Y _B 3HHM _B 3I5R _A PI3K(PIK3R2) 2KT1 _A 2XS6 _A 3MTT _A PRKACA 3AGM _A PRKAR2A 2IZX _A TNFα 1A8M _A 4TSV _A TNF-R1 1EXT _A 1ICH _A TP53 1AIE _A 1OLG _A 1XQH _B 1YC5 _B 2B3G _B 2FOO _B 2GS0 _B 2K8F _B 2VUK _A 3D06 _A 3DAB _B 3LW1 _P TRADD 1F3V _A TRAF2 1CZZ _A 1D00 _A 1F3V _B 3KNV _A 3M0A _A 3M0D _A TRAIL 1D4V _B 1DG6 _A 1DU3 _D TRAIL-R 1D4V _A 1DU3 _A TrkA 1HE7 _A 1SHC _B 1WWW _X 2IFG _A The abbreviations used are: AIF, apoptosis-inducing factor, mitochondrion-associated, 1 (AIFM1); AKT1, RAC-alpha serine/threonine-protein kinase; AKT2, RAC-beta serine/threonine-protein kinase; AKT3, RAC-gamma serine/threonine-protein kinase; APAF1, apoptotic peptidase activating factor 1; BCL-2, B-cell lymphoma 2; BCL-XL, BCL extra-large; BID, BH3 interacting domain death agonist; Bax, BCL-2-associated × protein; CASP3/6/7/8/9, caspase-3/6/7/8/9; Cn(CHP), calcineurin B homologous protein 1; Cn(CHP2), calcineurin B homologous protein 2; Cn(PPP3CA), protein phosphatase 3 catalytic subunit alpha isoform; Cn(PPP3R1), protein phosphatase 3 regulatory subunit 1; CytC, cytochrome C; DFF40, DNA fragmentation factor, 40kDa, beta polypeptide; DFF45, DNA fragmentation factor, 45kDa, alpha polypeptide; FADD, Fas-associated via death domain; FLIP, FLICE/CASP8 inhibitory protein (CASP8 and FADD-like apoptosis regulator, CFLAR); Fas, tumor necrosis factor receptor (TNF) superfamily member 6; IAP, inhibitor of apoptosis; BIRC2/3/4, baculoviral IAP repeat-containing protein 2/3/4; IκBα, nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor alpha; IKK, inhibitor of nuclear factor kappa-B kinase; IL-1(A), interleukin-1 alpha; IL-1(B), interleukin-1 beta; IL-1R(1), type 1 interleukin-1 receptor; IL-1R(RAP), interleukin-1 receptor accessory protein; IL-3, interleukin-3; IL-3R, interleukin-3 receptor; IRAK2/4, interleukin-1 receptor-associated kinase 2/4; MyD88, myeloid differentiation primary response protein MyD88; NF-κB(NFKB1), nuclear factor of kappa light polypeptide gene enhancer in B-cells; NF-κB(RELA), nuclear factor of kappa light polypeptide gene enhancer in B-cells 3; NGF, nerve growth factor (beta polypeptide); PI3K, phosphatidylinositide 3-kinase; PIK3CA, PI3K subunit alpha; PIK3CG, PI3K subunit gamma; PIK3R1, PI3K regulatory subunit alpha; PIK3R2, PI3K regulatory subunit beta; PRKACA, cyclic adenosine monophosphate (cAMP)-dependent protein kinase catalytic subunit alpha; PRKAR2A, cAMP-dependent protein kinase type II-alpha regulatory subunit; TNFα, tumor necrosis factor; TNF-R1, TNF receptor superfamily member 1A; TP53, cellular tumor antigen p53; TRADD, TNF receptor type 1-associated death domain protein; TRAF2, TNF receptor-associated factor 2; TRAIL, TNF receptor superfamily member 10; TRAIL-R, TNF receptor superfamily member 10B; TrkA, neurotrophic tyrosine kinase receptor type 1.

Publication Year: 2013


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4418667

No Compound Predicted score for Transcription factor NF-kappa B inhibitor activity Pa Pi 1 Boswellic acid 2e 0,735 0,002 2 Boswellic acid 2c 0,728 0,002 3 Boswellic acid 2d 0,717 0,002 4 Boswellic aci... 2a 0,691 0,003 5 Rehmannic acid 0,677 0,003 6 3b-trans-feruloyloxy-16b-hydroxylup-20(29)-ene 0,677 0,003 7 Boswellic acid 2b 0,676 0,003 8 Boswellic acid 2f 0,667 0,003 9 Glycyrrhetic acid 0,659 0,003 10 Sumaresinolic acid 0,656 0,003 11 Maniladiol 0,656 0,003 12 Boswellic acid 2g 0,648 0,003 13 Beta amyrin 0,648 0,003 14 Glycyrrhizin 0,641 0,003 15 Ursolic acid 0,638 0,003 16 Taraxerol acetate 0,635 0,003 17 Gymnemic acid I 0,633 0,003 18 Katonic acid 0,626 0,003 19 Imberbic acid 0,623 0,003 20 Oleanolic acid 0,620 0,003 21 3beta—acetoxy beta—amyrin 0,620 0,003 22 Coussaric acid 0,612 0,003 23 3 beta acetoxy alfa amyrin 0,607 0,003 24 Taraxasterol acetate 0,605 0,003 25 Alphitolic acid 0,603 0,004 26 Corosolic acid 0,597 0,004 27 Hederagenin 0,578 0,004 28 Madecassic acid 0,577 0,004 29 Augustic acid 0,577 0,004 30 2a,3a,19-trihydroxy-olean-12-en-23,28-dioic acid 0,568 0,004 31 2a,3a, 24-trihydroxyurs-12, 20(30)-dien-28-oic acid 0,568 0,004 32 Uvaol 0,567 0,004 33 Betunaldehyde 0,552 0,004 34 3b-trans-sinapoyloxylup-20(29)-en-28-ol 0,549 0,004 35 Asiatic acid 0,547 0,004 36 Emarginellic acid 0,545 0,004 37 3-O-acetylbetulinic acid 0,544 0,004 38 Polygalacic acid 0,541 0,004 39 Erythrodiol 0,541 0,004 40 Ursonic acid 0,540 0,004 41 Acetylursolic acid 0,539 0,004 42 Morolic acid 0,535 0,004 43 Arnidiol 0,532 0,004 44 Bartogenic acid 0,523 0,004 45 Barrinic acid 0,523 0,004 46 Barrigenic acid 0,523 0,004 47 19 epibartogenic acid 0,523 0,004 48 Hyptatic acid A 0,521 0,004 49 Bayogenin 0,521 0,004 50 Tanginol 0,512 0,004 51 Lupeol 0,511 0,004 52 CDDO methyl ester 0,502 0,005 53 Bryonolic acid 0,501 0,005 54 20-Epibryonolic acid 0,501 0,005 55 Germanicol 0,495 0,005 56 Faradiol 0,480 0,005 57 Crotalic acid 0,478 0,005 58 Betulinic acid 0,464 0,005 59 23-epoxy-friedelan-28-oic acid 0,460 0,005 60 Arjunoic acid 0,451 0,005 61 Pomolic acid 0,432 0,006 62 Impressic acid 0,427 0,006 63 Tangulic acid 0,422 0,006 64 Madecassoside 0,410 0,006 65 Canophyllal 0,403 0,007 66 Heliantriol C 0,395 0,007 67 CDDO 0,386 0,007 68 Anhydrobartogenic acid 0,384 0,007 69 Acutangulic acid 0,371 0,008 70 Asiaticoside 0,366 0,008 71 Phytolaccagenin 0,365 0,008 72 Amooranin 0,363 0,008 73 Rotundic acid 0,354 0,009 74 Friedeline 0,353 0,009 75 Euscaphic Acid (Tormantic acid) 0,352 0,009 76 Lupeol acetate 0,352 0,009 77 Epifriedelanol 0,339 0,009 78 Betulin 0,334 0,010 79 Tiarellic acid 0,311 0,011 80 Heliantriol B 0,308 0,011 81 Betulonic acid 0 , 298 0 , 012 82 3-oxo-friedelan-28-oic-acid 0 , 295 0 , 012 83 2a , 3ß , 19a , 23-tetrahydroxyurs-12-en-28-oic acid 0 , 293 0 , 012 84 Canophyllic acid 0 , 287 0 , 013 85 Zizyberanalic acid 0 , 286 0 , 013 86 Moronic acid 0 , 275 0 , 014 87 Rhoiptelenone 0 , 252 0 , 016 88 CDDO analoge 2-cyano-3 , 12-dioxooleana-1 , 9(11)-dien-28-onitrile 0 , 247 0 , 017 89 Glycyrrhetic acid 6c 0 , 242 0 , 018 90 24 hydroxy tormantic acid 0 , 240 0 , 018 91 Celastrol/ Tripterin 0 , 222 0 , 021 92 Goreishic acid I 0 , 219 0 , 022 93 Betulinic acid derivative 1 f 0 , 219 0 , 022 94 Zizyberenalic acid 0 , 215 0 , 023 95 Betulinic acid derivative 1 g 0 , 214 0 , 023 96 Canophyllol 0 , 212 0 , 024 97 2-amino-3-hydroxy-2-(hydroxymethyl) propyl betulonate 0 , 194 0 , 029 98 Ceanothic acid 0 , 184 0 , 032 99 Prisimerin 0 , 181 0 , 033 100 Pinfaenoic acid 0 , 180 0 , 034 101 24-hydroxybutulinic acid 0 , 165 0 , 039 102 Tingenone 0 , 155 0 , 044 103 CDDO-imidazolide 0 , 152 0 , 045 104 Goreishic acid II 0 , 152 0 , 045 105 N-(2 , 3-hydroxy-2-(hydroxymethyl) propyl) (3-O-acetyl) betulinamide 0 , 146 0 , 048 106 3-oxa-24-hydroxybutulinic acid 0 , 134 0 , 057 107 Tingenin 0 , 128 0 , 062 108 N-(2 , 3-hydroxy-2-(hydroxymethyl) propyl) betulinamide 0 , 112 0 , 081 109 Beta sitosterol 0 , 100 0 , 098 Compounds with Pa > 0.3 are highlighted in bold; compounds with Pa < 0.3 are highlighted in italic PTs dock on NEMO/IKKβ association complex where it binds to a steroidal lactone, Withaferin A The molecular model of the IKKβ for virtual screening was built using the x-ray co-crystal structure of NEMO/IKKβ association domain (PDB: 3BRV).

g001 Fig 1 Hydrogen bond interaction of CA (A), AA (B) and UA (C) at GLU 89 and SER 85 gatekeeper residues of NEMO/IKKβ association complex (PDB code: 3BRV).

On virtual screening, 109 PTs were screened through the PASS (prediction of activity spectra of substances) software for prediction of NF-κB inhibitory activity followed by docking on the NEMO/IKKβ association complex (PDB: 3BRV) and testing for compliance with the softened Lipinski’s Rule of Five using Schrodinger (LLC, New York, USA).

Before this report, the structure of a NEMO-IKKβ association complex (PDB: 3BRV) was used for docking studies of a steroidal phytoconstituent, Withaferin A [ 10 ].

These compounds were docked on IKKβ crystal structure retrieved from the Protein Data Bank [PDB: 3BRV] using the molecular docking software Glide (Version 5.5, Schrodinger, LLC, New York, USA, 2009) to determine its binding potential.

The crystal structure of the NEMO/IKKβ association domain was obtained from the RCSB Protein Data Bank (PDB) with the accession code 3BRV ( http://www.rcsb.org/pdb/explore/explore.do?structureId=3BRV ).

Publication Year: 2015