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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Binding site similarity measured by Shaper
You can zoom onto the graph by using the mouse to make a selection

Binding Sites are compared using Shaper.
For more information, please see the following publication: Desaphy J. et al. Comparison and Druggability Prediction of protein-Ligand Binding sites from pharmacophore-annotated cavity shapes J. Chem. Inf. Model., 2012, 52(8), pp2287-2299
Binding Sites are considered as similar when the similarity value is greater than 0.44

Reference Protein Data Bank Entry :
PDB IDHETUniprot NameEC Number
3nefPYVAbscisic acid receptor PYL1

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
3nefPYVAbscisic acid receptor PYL1/1.000
3zvuA8SAbscisic acid receptor PYR1/0.540
4la7A1OAbscisic acid receptor PYL2/0.539
3njoPYVAbscisic acid receptor PYR1/0.537
4ds8A8SAbscisic acid receptor PYL3/0.535
3r6pA8SAbscisic acid receptor PYL10/0.531
3nmnPYVAbscisic acid receptor PYL1/0.530
3negPYVAbscisic acid receptor PYL1/0.524
4lg5A1OAbscisic acid receptor PYL2/0.513
3ujlA8SAbscisic acid receptor PYL2/0.512
3kdjA8SAbscisic acid receptor PYL1/0.508
4oicA8SBet v I allergen-like/0.498
4lgaA2OAbscisic acid receptor PYL2/0.495
3kb3A8SAbscisic acid receptor PYL2/0.486
3k90A8SAbscisic acid receptor PYR1/0.485
3kdiA8SAbscisic acid receptor PYL2/0.485
3ns2PYVAbscisic acid receptor PYL2/0.485
3oquA8SAbscisic acid receptor PYL9/0.483
2hamC33Vitamin D3 receptor/0.481
3k3kA8SAbscisic acid receptor PYR1/0.481
1p93DEXGlucocorticoid receptor/0.479
4dscA8SAbscisic acid receptor PYL3/0.479
4fjz4FJPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.479
1ie9VDXVitamin D3 receptor/0.478
2hb8MVDVitamin D3 receptor/0.478
3a783EVVitamin D3 receptor/0.476
3njoP2MAbscisic acid receptor PYR1/0.475
3nmpPYVAbscisic acid receptor PYL2/0.473
2hasC3OVitamin D3 receptor/0.472
4iteTEYVitamin D3 receptor/0.472
3nj0PYVAbscisic acid receptor PYL2/0.470
3dpd41APhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.469
3nr4PYVAbscisic acid receptor PYL2/0.469
4gb90WRPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.468
4anx534Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.467
2z97CAMCamphor 5-monooxygenase1.14.15.10.466
1ie8KH1Vitamin D3 receptor/0.465
2fziDH3Dihydrofolate reductase1.5.1.30.465
2o4rVD5Vitamin D3 receptor/0.465
3vt45YIVitamin D3 receptor/0.465
4g1d0VKVitamin D3 receptor A/0.465
1txiTX5Vitamin D3 receptor/0.464
2chx090Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.464
2qblCAMCamphor 5-monooxygenase1.14.15.10.464
4l8u9AZSerum albumin/0.464
1phgMYTCamphor 5-monooxygenase1.14.15.10.463
1rk3VDXVitamin D3 receptor/0.463
2zlcVDXVitamin D3 receptor/0.463
3w9rA8SAbscisic acid receptor PYL9/0.463
1kb9SMACytochrome b/0.461
4ajwVWNPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform2.7.1.1530.461
4jlj1NMDeoxycytidine kinase2.7.1.740.461
4qa2SHHHistone deacetylase 83.5.1.980.461
4g1z0VPVitamin D3 receptor A/0.460
1kyoSMACytochrome b/0.459
1og5SWFCytochrome P450 2C9/0.459
2hb7O1CVitamin D3 receptor/0.459
3ojiPYVAbscisic acid receptor PYL3/0.459
4a9mP9MBromodomain-containing protein 2/0.459
4cd2FOLDihydrofolate reductase1.5.1.30.459
3kjsDQ1Bifunctional dihydrofolate reductase-thymidylate synthase/0.458
5cyqT27Gag-Pol polyprotein2.7.7.490.458
4o701QKBromodomain-containing protein 4/0.457
1rkhVD2Vitamin D3 receptor/0.456
2ydwWSHBromodomain-containing protein 2/0.456
3eej53RUncharacterized protein/0.456
3qly55VUncharacterized protein/0.456
3w0c6DSVitamin D3 receptor/0.456
4r20AERCytochrome P450 family 17 polypeptide 2/0.456
1rkgVD1Vitamin D3 receptor/0.455
3h3r14HCollagen type IV alpha-3-binding protein/0.455
2ibzSMACytochrome b/0.454
3fwfCAMCamphor 5-monooxygenase1.14.15.10.454
3h3sH15Collagen type IV alpha-3-binding protein/0.454
4c9pCAMCytochrome P450/0.454
4yaoFMNNADPH--cytochrome P450 reductase/0.454
3a1l2CCCytochrome P450/0.453
3vt65YIVitamin D3 receptor/0.453
3vt7VDXVitamin D3 receptor/0.453
3w0jT08Vitamin D3 receptor/0.453
1db1VDXVitamin D3 receptor/0.452
2hrcCHDFerrochelatase, mitochondrial4.99.1.10.452
2vn0TDZCytochrome P450 2C8/0.452
3u8hBHPPhospholipase A2, membrane associated/0.452
3w5tLHPVitamin D3 receptor/0.452
4g210VPVitamin D3 receptor A/0.452
4q0a4OAVitamin D3 receptor A/0.452
2e9cB75Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.451
3rukAERSteroid 17-alpha-hydroxylase/17,20 lyase/0.451
4hle17VPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.451
4ig3T27Gag-Pol polyprotein2.7.7.490.451
4uyf73BBromodomain-containing protein 2/0.451
1e7vLY2Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.450
1mvsDTMDihydrofolate reductase1.5.1.30.450
1upw444Oxysterols receptor LXR-beta/0.450
2po7CHDFerrochelatase, mitochondrial4.99.1.10.450
3qk0QK0Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.450
3sgv2BJDitrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.450
3w0hW12Vitamin D3 receptor/0.450
4a9iP9IBromodomain-containing protein 2/0.450
4fhi0S4Vitamin D3 receptor A/0.450
4h4o506Gag-Pol polyprotein2.7.7.490.450
1e8xATPPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.449
1nbmADPATP synthase subunit beta, mitochondrial3.6.3.140.449
3deyDHTEstradiol 17-beta-dehydrogenase 11.1.1.620.449
3klmDHTEstradiol 17-beta-dehydrogenase 11.1.1.620.449
3w0aDS5Vitamin D3 receptor/0.449
4ia3BIVVitamin D3 receptor A/0.449
4o761M3Bromodomain-containing protein 4/0.449
1fdwESTEstradiol 17-beta-dehydrogenase 11.1.1.620.448
2m56CAMCamphor 5-monooxygenase1.14.15.10.448
3cx5SMACytochrome b/0.448
3eek53SUncharacterized protein/0.448
3fwiCAMCamphor 5-monooxygenase1.14.15.10.448
3w0yDS4Vitamin D3 receptor/0.448
1xonPILcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.447
2chz093Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.447
3c0i3AMPeripheral plasma membrane protein CASK2.7.11.10.447
3cseN22Uncharacterized protein/0.447
3w5p4OAVitamin D3 receptor/0.447
4ezk0SDPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.447
4ia1BIVVitamin D3 receptor A/0.447
4nkvAERSteroid 17-alpha-hydroxylase/17,20 lyase/0.447
1aq1STUCyclin-dependent kinase 22.7.11.220.446
2feuCAMCamphor 5-monooxygenase1.14.15.10.446
2hc4VDXVitamin D3 receptor A/0.446
2hcdBIVVitamin D3 receptor A/0.446
2hk51BMTyrosine-protein kinase HCK2.7.10.20.446
2zbaZBATrichothecene 3-O-acetyltransferase/0.446
3vt9YI4Vitamin D3 receptor/0.446
4nky3QZSteroid 17-alpha-hydroxylase/17,20 lyase/0.446
4py6R78Bromodomain protein, putative/0.446
2y1oT26UDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.445
3inxJZCHeat shock protein HSP 90-alpha/0.445
3s7a684Dihydrofolate reductase1.5.1.30.445
3vrwYS5Vitamin D3 receptor/0.445
3vtcTK3Vitamin D3 receptor/0.445
4f1sF1SPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.445
1ezvSMACytochrome b/0.444
1y60H4M5,6,7,8-tetrahydromethanopterin hydro-lyase4.2.1.1470.444
2fzhDH1Dihydrofolate reductase1.5.1.30.444
2ovhAS0Progesterone receptor/0.444
3irxUDRGag-Pol polyprotein2.7.7.490.444
3zw3ZW3Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.444
4alhA9PBromodomain-containing protein 2/0.444
4anv751Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.444
4bewCZASarcoplasmic/endoplasmic reticulum calcium ATPase 13.6.3.80.444
4dpdDHFBifunctional dihydrofolate reductase-thymidylate synthase/0.444
4jlt8PRCytochrome P450 2B41.14.14.10.444
4l7sG7KTyrosine-protein kinase ITK/TSK2.7.10.20.444
1fmjRTLRetinol dehydratase/0.443
1j3iWRABifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.443
2hbhXE4Vitamin D3 receptor A/0.443
3fwgCAMCamphor 5-monooxygenase1.14.15.10.443
3vt5YI2Vitamin D3 receptor/0.443
3w5rLOAVitamin D3 receptor/0.443
4bchT7ZCyclin-dependent kinase 92.7.11.220.443
4h9506UDihydrofolate reductase1.5.1.30.443
4ia7BIVVitamin D3 receptor A/0.443
4iui1GQEstrogen receptor/0.443
4iwo1H4Serine/threonine-protein kinase TBK12.7.11.10.443
1a27ESTEstradiol 17-beta-dehydrogenase 11.1.1.620.442
1nooCAHCamphor 5-monooxygenase1.14.15.10.442
2hw2RFPRifampin ADP-ribosyl transferase/0.442
2j0vGDPRac-like GTP-binding protein ARAC7/0.442
2zl9VDAVitamin D3 receptor/0.442
3d0bSNXHeat shock protein HSP 90-alpha/0.442
3dmjGWEPol protein/0.442
3s1cZIRCytokinin dehydrogenase 11.5.99.120.442
3vrtYS2Vitamin D3 receptor/0.442
4g20484Vitamin D3 receptor A/0.442
4jib1L6cGMP-dependent 3',5'-cyclic phosphodiesterase3.1.4.170.442
4ure1PSCyclohexanol dehydrogenase/0.442
5d7pOCZNAD-dependent protein deacetylase sirtuin-23.5.10.442
2cd2FOLDihydrofolate reductase1.5.1.30.441
2qboCAMCamphor 5-monooxygenase1.14.15.10.441
3cxhSMACytochrome b/0.441
3lu8IQXSerum albumin/0.441
3m0eATPTranscriptional regulator (NtrC family)/0.441
3oafOAGDihydrofolate reductase1.5.1.30.441
4i2q1BTGag-Pol polyprotein2.7.7.490.441
4ia2BIVVitamin D3 receptor A/0.441
4oxyNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.441
4rujVDXVitamin D3 receptor A/0.441
1dz4CAMCamphor 5-monooxygenase1.14.15.10.440
1dz8CAMCamphor 5-monooxygenase1.14.15.10.440
1fm6BRLPeroxisome proliferator-activated receptor gamma/0.440
1l2jETCEstrogen receptor beta/0.440
2x7gPVBSRSF protein kinase 22.7.11.10.440
2yncYNCGlycylpeptide N-tetradecanoyltransferase/0.440
3iro2CYBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.440
3tk3CPZCytochrome P450 2B41.14.14.10.440
3vtbTKAVitamin D3 receptor/0.440
4ek1CAMCamphor 5-monooxygenase1.14.15.10.440
4h9814QUncharacterized protein/0.440
4qe6JN3Bile acid receptor/0.440
5d1bTSNHistone deacetylase 83.5.1.980.440