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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
4cfdS8YIntegrase

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
4cfdS8YIntegrase/1.000
4cf1IY7Integrase/0.670
4chqCWUIntegrase/0.631
4cfbOM3Integrase/0.598
3zt3ZT4Integrase/0.596
4cgiNZLIntegrase/0.596
4cjuJNSIntegrase/0.590
4ceoG0TIntegrase/0.589
4ck2NVUIntegrase/0.586
4cesNFWIntegrase/0.584
4cfaWOPIntegrase/0.584
4ced9NSIntegrase/0.575
4cefD0TIntegrase/0.574
4cjfRVNIntegrase/0.574
4ceaZSWIntegrase/0.573
4ceqQCHIntegrase/0.573
4cgd8P3Integrase/0.573
4cgjNZLIntegrase/0.567
3zswZSWIntegrase/0.566
3zsrO3NIntegrase/0.563
4cezO3NIntegrase/0.563
4cggK5QIntegrase/0.563
4cf0O5UIntegrase/0.560
4cjeQ31Integrase/0.558
4cerVL4Integrase/0.556
4cjkH39Integrase/0.555
4cf8V7HIntegrase/0.553
4cf23GMIntegrase/0.551
4cec2SSIntegrase/0.548
4cj54VWIntegrase/0.547
4cj3E4FIntegrase/0.543
4cfc7NVIntegrase/0.536
4chyC5QIntegrase/0.535
3zsqO4NIntegrase/0.534
4ck3K1TIntegrase/0.534
4ce9O3NIntegrase/0.533
4cieY7NIntegrase/0.533
4cifJDXIntegrase/0.532
3zszOM2Integrase/0.527
3zsxN44Integrase/0.526
4cj4S3GIntegrase/0.525
3zt0ZT0Integrase/0.524
4cjp4D2Integrase/0.522
4cghLOZIntegrase/0.521
4cigX0PIntegrase/0.519
4ck1OM1Integrase/0.519
3zsvZSVIntegrase/0.517
4cebZSVIntegrase/0.517
4ceeB0TIntegrase/0.517
4cjqVXOIntegrase/0.516
1kc1NDPdTDP-4-dehydrorhamnose reductase1.1.1.1330.505
3zt2ZT2Integrase/0.502
4cjrFYMIntegrase/0.502
3zt1OM1Integrase/0.500
1uxjNADMalate dehydrogenase/0.496
3zsyOM3Integrase/0.494
3zcmPX3Integrase/0.493
1pzgA3DLactate dehydrogenase/0.489
1ur5NADMalate dehydrogenase/0.476
2fn7NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase/0.475
4bkz1WSMaternal embryonic leucine zipper kinase2.7.11.10.473
2a94AP0L-lactate dehydrogenase1.1.1.270.472
1i24UPGUDP-sulfoquinovose synthase, chloroplastic3.13.1.10.471
1rx1NAPDihydrofolate reductase1.5.1.30.470
1rx8NAPDihydrofolate reductase1.5.1.30.470
3fhxPLPPyridoxal kinase2.7.1.350.469
3hdhNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.469
1f5fDHTSex hormone-binding globulin/0.467
3lpkZ76Beta-secretase 13.4.23.460.467
1uxkNADMalate dehydrogenase/0.466
4fv7E94Mitogen-activated protein kinase 12.7.11.240.466
1n2sNAIdTDP-4-dehydrorhamnose reductase1.1.1.1330.465
4cjsL0YIntegrase/0.465
3p82FMNPentaerythritol tetranitrate reductase/0.464
4eplJAIJasmonic acid-amido synthetase JAR16.3.20.464
2aa0MTPAdenosine kinase2.7.1.200.463
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.463
3lpiZ74Beta-secretase 13.4.23.460.463
3oibFDAPutative acyl-CoA dehydrogenase/0.463
4nbtNAD3-oxoacyl-[acyl-carrier-protein] reductase/0.463
1ia1NDPDihydrofolate reductase1.5.1.30.462
2ggsNDPdTDP-4-dehydrorhamnose reductase/0.462
3qt62P0Mevalonate diphosphate decarboxylase/0.462
1b8uNADMalate dehydrogenase/0.461
1e8xATPPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.461
2hdhNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.461
3otfCMPPotassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4/0.461
1pq944BOxysterols receptor LXR-beta/0.460
1sowNADL-lactate dehydrogenase1.1.1.270.460
2rh9IGPTryptophan synthase alpha chain/0.460
3nugNADPyridoxal 4-dehydrogenase1.1.1.1070.460
4y93746Tyrosine-protein kinase/0.460
1xe55FEPlasmepsin-23.4.23.390.459
2fznFADBifunctional protein PutA1.5.5.20.459
4k28NADShikimate dehydrogenase family protein/0.459
4z61ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.459
1h50FMNPentaerythritol tetranitrate reductase/0.458
1pzfA3DLactate dehydrogenase/0.458
2nrySTUInterleukin-1 receptor-associated kinase 42.7.11.10.458
2ohvNHLGlutamate racemase/0.458
4q71FADBifunctional protein PutA/0.458
5a3bAPRSIR2 family protein/0.458
3p62FMNPentaerythritol tetranitrate reductase/0.457
1a59COA2-methylcitrate synthase/0.456
3g5qFADMethylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO/0.456
3lsiFADPyranose 2-oxidase/0.456
4cr8NADN-acylmannosamine 1-dehydrogenase1.1.1.2330.456
2chx090Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.455
3kjrNAPBifunctional dihydrofolate reductase-thymidylate synthase/0.455
3tjzGNPADP-ribosylation factor 1/0.455
3vjoANPEpidermal growth factor receptor2.7.10.10.455
4c02TAKActivin receptor type-12.7.11.300.455
4gj30XPNon-receptor tyrosine-protein kinase TYK22.7.10.20.455
1h63FMNPentaerythritol tetranitrate reductase/0.454
1hbvGANGag-Pol polyprotein/0.454
1p0hACOMycothiol acetyltransferase2.3.1.1890.454
4b8zNAPGDP-L-fucose synthase1.1.1.2710.454
4z64ILE_THR_GLN_TYS_TYSPhytosulfokine receptor 12.7.11.10.454
3b6zCO7Enoyl reductase LovC10.453
3giyFMN(S)-mandelate dehydrogenase1.1.99.310.453
3mknDNBPyrimidine-specific ribonucleoside hydrolase RihB/0.453
4ajn88VL-lactate dehydrogenase A chain1.1.1.270.453
4c7kNAPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.453
4gh5NADShort-chain dehydrogenase/reductase SDR/0.453
4nd3NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase/0.453
1t2dNADL-lactate dehydrogenase1.1.1.270.452
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.452
4ure1PSCyclohexanol dehydrogenase/0.452
1a4rGNHCell division control protein 42 homolog/0.451
1j4jACOAcetyltransferase2.3.10.451
1me6IVSPlasmepsin-23.4.23.390.451
2c27ACOMycothiol acetyltransferase2.3.1.1890.451
2q2qNADBeta-D-hydroxybutyrate dehydrogenase/0.451
2ztvNADD(-)-3-hydroxybutyrate dehydrogenase/0.451
3ndrNADPyridoxal 4-dehydrogenase1.1.1.1070.451
4du82P0Mevalonate diphosphate decarboxylase/0.451
4rosAPRMalate dehydrogenase/0.451
5a4kFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.451
5b1yNDP3-oxoacyl-[acyl-carrier-protein] reductase/0.451
1h51FMNPentaerythritol tetranitrate reductase/0.450
1jtvTESEstradiol 17-beta-dehydrogenase 11.1.1.620.450
1powFADPyruvate oxidase1.2.3.30.450
2w9hTOPDihydrofolate reductase1.5.1.30.450
4ewn0VRImidazole glycerol phosphate synthase subunit HisF4.1.30.450
4j7xNAPSepiapterin reductase1.1.1.1530.450
4kz01UJPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.450
4l4xNDPAmphI/0.450
4rrvATP3-phosphoinositide-dependent protein kinase 12.7.11.10.450
1di8DTQCyclin-dependent kinase 22.7.11.220.449
1e6wNAD3-hydroxyacyl-CoA dehydrogenase type-21.1.1.350.449
1qrpHH0Pepsin A-43.4.23.10.449
3sf6FDAGlutaryl-CoA dehydrogenase/0.449
4e8yIHAD-beta-D-heptose 7-phosphate kinase/0.449
4ejn0R4RAC-alpha serine/threonine-protein kinase2.7.11.10.449
4h3qANPMitogen-activated protein kinase 12.7.11.240.449
1d4aFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.448
1svlADPLarge T antigen3.6.40.448
1wwkNAD307aa long hypothetical phosphoglycerate dehydrogenase/0.448
3dxmN24Actin-related protein 3/0.448
3em3478Gag-Pol polyprotein3.4.23.160.448
3hadNADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial1.1.1.350.448
3v2uATPProtein GAL3/0.448
3vrwYS5Vitamin D3 receptor/0.448
3zvvXAZPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.448
4anx534Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.448
1dr3HBIDihydrofolate reductase1.5.1.30.447
1pd9CO4Dihydrofolate reductase1.5.1.30.447
1pzhNADLactate dehydrogenase/0.447
4dptAGSMevalonate diphosphate decarboxylase/0.447
4m4922YL-lactate dehydrogenase A chain1.1.1.270.447
4nd2A3DLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase/0.447
4zlaBESCytosol aminopeptidase3.4.11.10.447
1hdcCBO3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase1.1.1.530.446
1nzdUPGDNA beta-glucosyltransferase/0.446
1tj0FADBifunctional protein PutA1.5.5.20.446
1zemNADXylitol dehydrogenase/0.446
2d1yNADOxidoreductase, short-chain dehydrogenase/reductase family/0.446
3kb6NADD-lactate dehydrogenase/0.446
3lqfNADGalactitol dehydrogenase/0.446
4gyy12VUDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit/0.446
1cjuFOKAdenylate cyclase type 2/0.445
1cjuFOKAdenylate cyclase type 5/0.445
1jpaANPEphrin type-B receptor 22.7.10.10.445
1k8y13PTryptophan synthase alpha chain/0.445
1sq5ADPPantothenate kinase2.7.1.330.445
1w6hTITPlasmepsin-23.4.23.390.445
2xs0ANPMitogen-activated protein kinase 82.7.11.240.445
3nuuJOZ3-phosphoinositide-dependent protein kinase 12.7.11.10.445
3owaFADAcyl-CoA dehydrogenase/0.445
3t2vKKJPeptidoglycan recognition protein 1/0.445
4bqpNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.445
4e2dFMNDehydrogenase/0.445
4fhd0TTSpore photoproduct lyase/0.445
4fhk0U0Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.445
4wh2ADPN-acetylhexosamine 1-kinase2.7.1.1620.445
4y3jHICEndothiapepsin3.4.23.220.445
1guyNADMalate dehydrogenase/0.444
1gzuNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 12.7.7.10.444
1kfbIGPTryptophan synthase alpha chain/0.444
1mzs6693-oxoacyl-[acyl-carrier-protein] synthase 3/0.444
1nlmUD1UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase/0.444
1nytNAPShikimate dehydrogenase (NADP(+))/0.444
1zrzBI1Protein kinase C iota type2.7.11.130.444
2q9fC3SCholesterol 24-hydroxylase/0.444
2wyvNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.444
2y9qANPMitogen-activated protein kinase 12.7.11.240.444
2znq401Peroxisome proliferator-activated receptor delta/0.444
3d84NDPDihydrofolate reductase1.5.1.30.444
3dheANDEstradiol 17-beta-dehydrogenase 11.1.1.620.444
3docNADGlyceraldehyde-3-phosphate dehydrogenase/0.444
3em0CHDFatty acid-binding protein 6, ileal (gastrotropin)/0.444
3f03FMNPentaerythritol tetranitrate reductase/0.444
3lfm3DTAlpha-ketoglutarate-dependent dioxygenase FTO/0.444
3o26NDPSalutaridine reductase/0.444
5hes032Mitogen-activated protein kinase kinase kinase 202.7.11.250.444
1bdlIM1Gag-Pol polyprotein3.4.23.160.443
1gcoNADGlucose 1-dehydrogenase1.1.1.470.443
1siqFADGlutaryl-CoA dehydrogenase, mitochondrial1.3.8.60.443
2brbPFQSerine/threonine-protein kinase Chk12.7.11.10.443
2e9uA25Serine/threonine-protein kinase Chk12.7.11.10.443
2rbeNDPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.443
2vttLZDCyclin-dependent kinase 22.7.11.220.443
3gu83GUDeath-associated protein kinase 12.7.11.10.443
3iaeD7KBenzaldehyde lyase/0.443
3otwCOAPhosphopantetheine adenylyltransferase/0.443
3zw9NADPeroxisomal bifunctional enzyme1.1.1.350.443
4ajp88NL-lactate dehydrogenase A chain1.1.1.270.443
4e8wIHAD-beta-D-heptose 7-phosphate kinase/0.443
4jnkZHKL-lactate dehydrogenase A chain1.1.1.270.443
4kip1R9Mitogen-activated protein kinase 14/0.443
4lcjNADC-terminal-binding protein 2/0.443
1ay0TPPTransketolase 12.2.1.10.442
1drhNAPDihydrofolate reductase1.5.1.30.442
1fm4DXCMajor pollen allergen Bet v 1-L/0.442
1n4pCYS_VAL_ILE_LEU_GERGeranylgeranyl transferase type-1 subunit beta2.5.1.590.442
2clqSTUMitogen-activated protein kinase kinase kinase 52.7.11.250.442
2ejvNADL-threonine 3-dehydrogenase/0.442
2nruT12Interleukin-1 receptor-associated kinase 42.7.11.10.442
2xckMH43-phosphoinositide-dependent protein kinase 12.7.11.10.442
2xrwANPMitogen-activated protein kinase 82.7.11.240.442
3b70NAPEnoyl reductase LovC10.442
3sp6IL2Peroxisome proliferator-activated receptor alpha/0.442
3uxyNADShort-chain dehydrogenase/reductase SDR/0.442
3vfqAR6Poly [ADP-ribose] polymerase 142.4.2.300.442
4a83DXCMajor pollen allergen Bet v 1-A/0.442
4e2bFMNDehydrogenase/0.442
4eagATP5'-AMP-activated protein kinase subunit gamma-1/0.442
4eudCOASuccinyl-CoA:acetate CoA-transferase/0.442
4n6bCOAUncharacterized protein/0.442
4q73FADBifunctional protein PutA/0.442
4qzuRTLRetinol-binding protein 2/0.442
4wxg2BOSerine hydroxymethyltransferase/0.442
1ea0FMNGlutamate synthase [NADPH] large chain1.4.1.130.441
1equEQIEstradiol 17-beta-dehydrogenase 11.1.1.620.441
1gg5FADNAD(P)H dehydrogenase [quinone] 11.6.5.20.441
1luaNAPBifunctional protein MdtA1.5.1.50.441
2brnDF1Serine/threonine-protein kinase Chk12.7.11.10.441
2c29NAPDihydroflavonol 4-reductase/0.441
2tpsTPSThiamine-phosphate synthase/0.441
2y05NAPProstaglandin reductase 1/0.441
3au8NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic1.1.1.2670.441
3vw6IM6Mitogen-activated protein kinase kinase kinase 52.7.11.250.441
4dpuAGSMevalonate diphosphate decarboxylase/0.441
4j7uNAPSepiapterin reductase1.1.1.1530.441
4kh0ATPAspartate carbamoyltransferase regulatory chain {ECO:0000256|HAMAP-Rule:MF_00002}/0.441
4q72FADBifunctional protein PutA/0.441
4wda2AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.441
1cjtFOKAdenylate cyclase type 2/0.440
1cjtFOKAdenylate cyclase type 5/0.440
1rfuADPPyridoxal kinase2.7.1.350.440
1udaUFGUDP-glucose 4-epimerase5.1.3.20.440
1z7yAA5Cysteine synthase 12.5.1.470.440
2d29FADAcyl-CoA dehydrogenase/0.440
2gv8NDPThiol-specific monooxygenase1.14.130.440
2qn3F55Glycogen phosphorylase, muscle form2.4.1.10.440
2rhgIGPTryptophan synthase alpha chain/0.440
2z1qFADAcyl-CoA dehydrogenase/0.440
3bgcLJHGag-Pol polyprotein3.4.23.160.440
3dv3MEKDual specificity mitogen-activated protein kinase kinase 12.7.12.20.440
3wb2YGPUncharacterized protein MJ0488/0.440
4i1iNADMalate dehydrogenase/0.440
5ar4SB2Receptor-interacting serine/threonine-protein kinase 22.7.11.10.440
5dp2NAPCurF/0.440