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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Cavity similarities measured by Shaper
You can zoom onto the graph by using the mouse to make a selection

Cavities 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

Reference Protein Data Bank Entry :
PDB ID HET Uniprot Name EC Number
4hmbPZZPhospholipase A2 VRV-PL-VIIIa

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
4hmbPZZPhospholipase A2 VRV-PL-VIIIa/1.000
1th6OINBasic phospholipase A2 VRV-PL-VIIIa3.1.1.40.625
4qemHC4Phospholipase A2 VRV-PL-VIIIa/0.621
2oliIOPBasic phospholipase A2 VRV-PL-VIIIa3.1.1.40.617
2othNIMBasic phospholipase A2 VRV-PL-VIIIa3.1.1.40.617
4qerSTLPhospholipase A2 VRV-PL-VIIIa/0.607
2qvdBERBasic phospholipase A2 VRV-PL-VIIIa3.1.1.40.606
4eixNIMPhospholipase A2 VRV-PL-VIIIa/0.569
2pwsIBPBasic phospholipase A2 VRV-PL-VIIIa3.1.1.40.559
2oyfIACBasic phospholipase A2 VRV-PL-VIIIa3.1.1.40.556
3u8dU8DPhospholipase A2, membrane associated/0.551
1db48INPhospholipase A2, membrane associated/0.548
1dcyI3NPhospholipase A2, membrane associated/0.543
4qf7C0RPhospholipase A2 VRV-PL-VIIIa/0.535
1kquBR4Phospholipase A2, membrane associated/0.534
1skgVAL_ALA_PHE_ARG_SERBasic phospholipase A2 VRV-PL-VIIIa3.1.1.40.532
3fo7IMNPhospholipase A2 VRV-PL-VIIIa/0.532
1db56INPhospholipase A2, membrane associated/0.530
5p2pDHGPhospholipase A2, major isoenzyme3.1.1.40.511
2qhwPZZBasic phospholipase A2 VRV-PL-VIIIa3.1.1.40.503
3sqwANPATP-dependent RNA helicase MSS116, mitochondrial3.6.4.130.491
3i5xANPATP-dependent RNA helicase MSS116, mitochondrial3.6.4.130.478
1y6oMJIPhospholipase A2, major isoenzyme3.1.1.40.473
4qgdPZZPhospholipase A2 VRV-PL-VIIIa/0.470
4olfHFGProline--tRNA ligase6.1.1.150.468
1v79FR7Adenosine deaminase3.5.4.40.465
3h3t16HCollagen type IV alpha-3-binding protein/0.465
2cdaNAPGlucose 1-dehydrogenase/0.464
3h3qH13Collagen type IV alpha-3-binding protein/0.463
1ndzFR5Adenosine deaminase3.5.4.40.461
2bikBI1Serine/threonine-protein kinase pim-12.7.11.10.460
5c8a5ADProbable transcriptional regulator/0.458
4rslFADFructosyl peptide oxidase/0.455
3njuANNAcidic phospholipase A2 33.1.1.40.454
3pe2E1BCasein kinase II subunit alpha2.7.11.10.454
3bgxMEFThymidylate synthase/0.453
2qd3CHDFerrochelatase, mitochondrial4.99.1.10.452
1z6tADPApoptotic protease-activating factor 1/0.451
2hk9NAPShikimate dehydrogenase (NADP(+))/0.451
2ojg19AMitogen-activated protein kinase 12.7.11.240.451
1rfuADPPyridoxal kinase2.7.1.350.450
3bgxTMPThymidylate synthase/0.450
4k9yK9YFocal adhesion kinase 12.7.10.20.450
1srfMTBStreptavidin/0.449
2qhxFE1Pteridine reductase 11.5.1.330.449
2z0ySAMRibosomal RNA small subunit methyltransferase E/0.449
3ivcFG4Pantothenate synthetase6.3.2.10.449
4othDRNSerine/threonine-protein kinase N1/0.448
3vjcZGASqualene synthase2.5.1.210.447
4dquNAIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.447
3p74FMNPentaerythritol tetranitrate reductase/0.446
3t5iSER_SER_CMT_FARRetinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta/0.446
2zb45OPProstaglandin reductase 21.3.1.480.445
4xf7ACPCarbohydrate/pyrimidine kinase, PfkB family/0.445
2ga9AGSPoly(A) polymerase catalytic subunit2.7.7.190.444
1umlFR4Adenosine deaminase3.5.4.40.443
2fm5M99cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.443
3njoPYVAbscisic acid receptor PYR1/0.443
4aosFADSteroid monooxygenase/0.443
4g8jTHMUridine phosphorylase/0.443
1dggNDPCatalase1.11.1.60.442
1fwkADPHomoserine kinase2.7.1.390.442
1xorZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.442
3acy702Dehydrosqualene synthase/0.442
3cmfPDN3-oxo-5-beta-steroid 4-dehydrogenase/0.442
3er93ATPoly(A) polymerase catalytic subunit2.7.7.190.442
3o56ZG1cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.442
3prfFP3Serine/threonine-protein kinase B-raf2.7.11.10.442
4a8v2ANMajor pollen allergen Bet v 1-J/0.442
4qa0SHHHistone deacetylase 83.5.1.980.442
2z7gEH9Adenosine deaminase3.5.4.40.441
2zseACPPantothenate kinase2.7.1.330.441
3fowIMHPurine nucleoside phosphorylase/0.441
2fb8215Serine/threonine-protein kinase B-raf2.7.11.10.440
2j0vGDPRac-like GTP-binding protein ARAC7/0.440
3h3sH15Collagen type IV alpha-3-binding protein/0.440
3zhqTPPMultifunctional 2-oxoglutarate metabolism enzyme1.2.4.20.440
4gevCB3Thymidylate synthase/0.440