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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
4hmbPZZPhospholipase A2 VRV-PL-VIIIa

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
4hmbPZZPhospholipase A2 VRV-PL-VIIIa/1.000
4qemHC4Phospholipase A2 VRV-PL-VIIIa/0.639
4qerSTLPhospholipase A2 VRV-PL-VIIIa/0.616
2qvdBERBasic phospholipase A2 VRV-PL-VIIIa3.1.1.40.610
2oliIOPBasic phospholipase A2 VRV-PL-VIIIa3.1.1.40.608
1aypINBPhospholipase A2, membrane associated/0.580
1db48INPhospholipase A2, membrane associated/0.571
3u8hBHPPhospholipase A2, membrane associated/0.555
1dcyI3NPhospholipase A2, membrane associated/0.554
3u8dU8DPhospholipase A2, membrane associated/0.554
1kvoOAPPhospholipase A2, membrane associated/0.553
2oyfIACBasic phospholipase A2 VRV-PL-VIIIa3.1.1.40.551
4eixNIMPhospholipase A2 VRV-PL-VIIIa/0.546
2pwsIBPBasic phospholipase A2 VRV-PL-VIIIa3.1.1.40.544
1kquBR4Phospholipase A2, membrane associated/0.543
1db56INPhospholipase A2, membrane associated/0.541
1skgVAL_ALA_PHE_ARG_SERBasic phospholipase A2 VRV-PL-VIIIa3.1.1.40.541
2othNIMBasic phospholipase A2 VRV-PL-VIIIa3.1.1.40.541
4qf7C0RPhospholipase A2 VRV-PL-VIIIa/0.529
2qhwPZZBasic phospholipase A2 VRV-PL-VIIIa3.1.1.40.520
5p2pDHGPhospholipase A2, major isoenzyme3.1.1.40.516
3sqwANPATP-dependent RNA helicase MSS116, mitochondrial3.6.4.130.503
3i5xANPATP-dependent RNA helicase MSS116, mitochondrial3.6.4.130.493
4qgdPZZPhospholipase A2 VRV-PL-VIIIa/0.490
1y6oMJIPhospholipase A2, major isoenzyme3.1.1.40.481
2bikBI1Serine/threonine-protein kinase pim-12.7.11.10.481
4olfHFGProline--tRNA ligase6.1.1.150.479
2cdaNAPGlucose 1-dehydrogenase/0.478
3njuANNAcidic phospholipase A2 33.1.1.40.477
4aosFADSteroid monooxygenase/0.477
1v79FR7Adenosine deaminase3.5.4.40.473
4k9yK9YFocal adhesion kinase 12.7.10.20.473
1ndzFR5Adenosine deaminase3.5.4.40.472
2ojg19AMitogen-activated protein kinase 12.7.11.240.472
1cjtFOKAdenylate cyclase type 2/0.470
1cjtFOKAdenylate cyclase type 5/0.470
4xwtU5PRibonuclease J/0.469
3acy702Dehydrosqualene synthase/0.468
2z7gEH9Adenosine deaminase3.5.4.40.467
4a87NARMajor pollen allergen Bet v 1-A/0.467
4plpNADHomospermidine synthase2.5.1.440.467
4xf7ACPCarbohydrate/pyrimidine kinase, PfkB family/0.467
1rfuADPPyridoxal kinase2.7.1.350.466
1srfMTBStreptavidin/0.465
1fxfMJIPhospholipase A2, major isoenzyme3.1.1.40.464
3bgxMEFThymidylate synthase/0.464
3h3t16HCollagen type IV alpha-3-binding protein/0.464
4othDRNSerine/threonine-protein kinase N1/0.464
1z6tADPApoptotic protease-activating factor 1/0.463
2qhxFE1Pteridine reductase 11.5.1.330.463
3acw651Dehydrosqualene synthase/0.463
4c1iEH9cGMP-dependent 3',5'-cyclic phosphodiesterase3.1.4.170.463
2ga9AGSPoly(A) polymerase catalytic subunit2.7.7.190.462
3pe2E1BCasein kinase II subunit alpha2.7.11.10.462
1bsvNDPGDP-L-fucose synthase/0.461
1dggNDPCatalase1.11.1.60.461
1umlFR4Adenosine deaminase3.5.4.40.460
4g090VDHistidinol dehydrogenase/0.460
1cjuFOKAdenylate cyclase type 2/0.459
1cjuFOKAdenylate cyclase type 5/0.459
4bfwZVWPantothenate kinase2.7.1.330.459
1ezfIN0Squalene synthase2.5.1.210.458
1zeoC01Peroxisome proliferator-activated receptor gamma/0.458
3prfFP3Serine/threonine-protein kinase B-raf2.7.11.10.458
3sqxANPATP-dependent RNA helicase MSS116, mitochondrial3.6.4.130.458
4a86H35Major pollen allergen Bet v 1-A/0.458
2z0ySAMRibosomal RNA small subunit methyltransferase E/0.456
3qm4PN0Cytochrome P450 2D6/0.456
1cjvFOKAdenylate cyclase type 2/0.455
1cjvFOKAdenylate cyclase type 5/0.455
3hk1B64Fatty acid-binding protein, adipocyte/0.455
3o56ZG1cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.454
4hni16WCasein kinase I isoform epsilon2.7.11.10.454
1cjkFOKAdenylate cyclase type 2/0.453
1cjkFOKAdenylate cyclase type 5/0.453
1cqp803Integrin alpha-L/0.453
1kzuRG1Light-harvesting protein B-800/850 alpha chain/0.453
1kzuRG1Light-harvesting protein B-800/850 beta chain/0.453
1v7aFRCAdenosine deaminase3.5.4.40.453
2e0nSAHPrecorrin-2 C20-methyltransferase/0.453
3ofm4B0Casein kinase II subunit alpha'2.7.11.10.453
4tzk641Enoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.453
1mczRMNBenzoylformate decarboxylase4.1.1.70.452
1qxlFR8Adenosine deaminase3.5.4.40.452
3er93ATPoly(A) polymerase catalytic subunit2.7.7.190.452
4ea13RXDehydrosqualene synthase/0.451
1xomCIOcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.450
2b365PPEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.450
3bw4FMNPutative 2-nitropropane dioxygenase/0.450
3d74NBBPheromone-binding protein ASP1/0.450
3h3sH15Collagen type IV alpha-3-binding protein/0.450
3ielU5PRibonuclease TTHA02523.10.450
4b7dQLECytochrome P450 monooxygenase PikC/0.450
4cukNAID-lactate dehydrogenase/0.450
4eufNADTrans-2-enoyl-CoA reductase [NADH]/0.450
1tl7FOKAdenylate cyclase type 2/0.449
1tl7FOKAdenylate cyclase type 5/0.449
3cmfPDN3-oxo-5-beta-steroid 4-dehydrogenase/0.449
4az29MUProthrombin3.4.21.50.449
4b144XBGlycylpeptide N-tetradecanoyltransferase/0.449
4r81FMNPredicted NADH dehydrogenase/0.449
3reyXACAdenosine receptor A2a/0.449
1rfvADPPyridoxal kinase2.7.1.350.448
1zgaHMKIsoflavone 4'-O-methyltransferase/0.448
2cd8PXICytochrome P450 monooxygenase PikC/0.448
2fm5M99cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.448
2pauD5M5'-deoxynucleotidase YfbR/0.448
2wsa646Glycylpeptide N-tetradecanoyltransferase/0.448
3zsh469Mitogen-activated protein kinase 14/0.448
4bbhYBNGlycylpeptide N-tetradecanoyltransferase/0.448
4g67SAHUncharacterized ACR, COG1565 superfamily/0.448
1mkdZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.447
1tezFADDeoxyribodipyrimidine photo-lyase4.1.99.30.447
2rtqIMIStreptavidin/0.447
3c0g3AMPeripheral plasma membrane protein CASK2.7.11.10.447
4b6l9ZPSerine/threonine-protein kinase PLK32.7.11.210.447
4bgg844Activin receptor type-12.7.11.300.447
4dquNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.447
4dymIYZActivin receptor type-12.7.11.300.447
4ia2BIVVitamin D3 receptor A/0.447
4lxjLANLanosterol 14-alpha demethylase1.14.13.700.447
5dqrFAD7-hydroxymethyl chlorophyll a reductase, chloroplastic1.17.7.20.447
5fm7ADPRuvB-like helicase/0.447
2bgiFADNADPH:ferredoxin reductase/0.446
2rabNADGlutathione amide reductase/0.446
2rtmIMIStreptavidin/0.446
2xweAMFGlucosylceramidase3.2.1.450.446
3bw2FMNPutative 2-nitropropane dioxygenase/0.446
3h3r14HCollagen type IV alpha-3-binding protein/0.446
3ituIBMcGMP-dependent 3',5'-cyclic phosphodiesterase3.1.4.170.446
3mtfA3FActivin receptor type-12.7.11.300.446
3ncz3NCRho-associated protein kinase 12.7.11.10.446
3upkUD1UDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.446
3w1wCHDFerrochelatase, mitochondrial4.99.1.10.446
4c02TAKActivin receptor type-12.7.11.300.446
4gqkADPActin cross-linking toxin VgrG1/0.446
4j521J3Serine/threonine-protein kinase PLK12.7.11.210.446
4o7uTHFThymidylate synthase/0.446
1wxyFRKAdenosine deaminase3.5.4.40.445
2fb8215Serine/threonine-protein kinase B-raf2.7.11.10.445
3bhrTHGThymidylate synthase/0.445
3biz61EWee1-like protein kinase2.7.10.20.445
3h3qH13Collagen type IV alpha-3-binding protein/0.445
3nmpPYVAbscisic acid receptor PYL2/0.445
4dfn0K1Tyrosine-protein kinase SYK2.7.10.20.445
4nieNBHNuclear receptor ROR-gamma/0.445
5c6cCMPcGMP-dependent protein kinase 22.7.11.120.445
1u1cBAUUridine phosphorylase2.4.2.30.444
1xwsBI1Serine/threonine-protein kinase pim-12.7.11.10.444
3byzH11Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.444
3vf80JETyrosine-protein kinase SYK2.7.10.20.444
4ea2RWZDehydrosqualene synthase/0.444
5epeSAHUncharacterized protein/0.444
2uagUMAUDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.443
3tfn2CJDehydrosqualene synthase/0.443
1bwlFMNNADPH dehydrogenase 11.6.99.10.442
1ejiTHFSerine hydroxymethyltransferase, cytosolic/0.442
2z3uCRRCytochrome P450/0.442
3cylVITBasic phospholipase A2 homolog piratoxin-2/0.442
3tfp03LDehydrosqualene synthase/0.442
4ax9N5NProthrombin3.4.21.50.442
4da8BG2Purine nucleoside phosphorylase DeoD-type2.4.2.10.442
4lxb7R9Prothrombin3.4.21.50.442
4u9zCOAAlpha-tubulin N-acetyltransferase 1/0.442
1synF89Thymidylate synthase/0.441
1vzqSHYProthrombin3.4.21.50.441
1x2hLPALipoate-protein ligase A6.3.1.200.441
2chx090Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.441
2f99AKVAklanonic acid methyl ester cyclase AcmA5.5.1.230.441
2q5qKPVIndole-3-pyruvate decarboxylase4.1.1.740.441
2rtoIMIStreptavidin/0.441
3c3xNAPEugenol synthase 11.1.1.3180.441
3g4iD71cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.441
3jyqNADQuinate/shikimate dehydrogenase (NAD(+))/0.441
3p74FMNPentaerythritol tetranitrate reductase/0.441
3zhqTPPMultifunctional 2-oxoglutarate metabolism enzyme1.2.4.20.441
4ewqMWLMitogen-activated protein kinase 14/0.441
4fevPP1Aminoglycoside 3'-phosphotransferase AphA1-IAB/0.441
4relKMPGlycosyltransferase/0.441
4xiwAZMCarbonic anhydrase, alpha type/0.441
4zhiADPKinesin-like protein KIF11/0.441
1e7qNAPGDP-L-fucose synthase/0.440
1fm7DFVChalcone--flavonone isomerase 15.5.1.60.440
1x1cSAHC-20 methyltransferase/0.440
1x8lOXRRetinol dehydratase/0.440
2gqg1N1Tyrosine-protein kinase ABL12.7.10.20.440
2j5sKTAAlr4455 protein/0.440
2nmtMIMGlycylpeptide N-tetradecanoyltransferase2.3.1.970.440
2v19FMNDodecin/0.440
3r04UNQSerine/threonine-protein kinase pim-12.7.11.10.440
4bftZVTPantothenate kinase2.7.1.330.440
4dliIRGMitogen-activated protein kinase 14/0.440
4ia3BIVVitamin D3 receptor A/0.440
5d7q4I5NAD-dependent protein deacetylase sirtuin-23.5.10.440