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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
4ceoG0TIntegrase

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
4ceoG0TIntegrase/1.000
4cf8V7HIntegrase/0.757
3zsrO3NIntegrase/0.677
4cezO3NIntegrase/0.677
4ceqQCHIntegrase/0.641
4cerVL4Integrase/0.631
4cesNFWIntegrase/0.603
4ced9NSIntegrase/0.597
4cj3E4FIntegrase/0.596
4cec2SSIntegrase/0.594
4cjuJNSIntegrase/0.588
4cgd8P3Integrase/0.583
4ceaZSWIntegrase/0.581
3zt0ZT0Integrase/0.580
3zsvZSVIntegrase/0.575
4cebZSVIntegrase/0.575
4ceeB0TIntegrase/0.572
4cf23GMIntegrase/0.569
4cfbOM3Integrase/0.569
4cefD0TIntegrase/0.567
4cgiNZLIntegrase/0.567
4cigX0PIntegrase/0.566
4cggK5QIntegrase/0.565
4cgjNZLIntegrase/0.565
4ce9O3NIntegrase/0.562
4chyC5QIntegrase/0.562
4cfdS8YIntegrase/0.561
4cghLOZIntegrase/0.561
3zswZSWIntegrase/0.559
3zsqO4NIntegrase/0.558
4cjeQ31Integrase/0.554
4cjrFYMIntegrase/0.553
4cfaWOPIntegrase/0.551
3zsyOM3Integrase/0.548
4cf0O5UIntegrase/0.548
4cjfRVNIntegrase/0.546
4ck1OM1Integrase/0.544
3zt3ZT4Integrase/0.543
4cf1IY7Integrase/0.543
4cjsL0YIntegrase/0.541
4cieY7NIntegrase/0.538
4cifJDXIntegrase/0.534
4cjkH39Integrase/0.533
3zszOM2Integrase/0.531
3zsxN44Integrase/0.528
4cjqVXOIntegrase/0.528
4ck2NVUIntegrase/0.522
4cj4S3GIntegrase/0.520
4cjp4D2Integrase/0.520
3zt2ZT2Integrase/0.516
4cfc7NVIntegrase/0.515
4chqCWUIntegrase/0.515
4ck3K1TIntegrase/0.504
3zcmPX3Integrase/0.503
3zt1OM1Integrase/0.501
4cj54VWIntegrase/0.499
1rx8NAPDihydrofolate reductase1.5.1.30.493
2cchATPCyclin-dependent kinase 22.7.11.220.482
2w9hTOPDihydrofolate reductase1.5.1.30.475
1u4oNDDL-lactate dehydrogenase1.1.1.270.470
2briANPUridylate kinase2.7.4.220.469
1mvsDTMDihydrofolate reductase1.5.1.30.468
1di8DTQCyclin-dependent kinase 22.7.11.220.467
1jtvTESEstradiol 17-beta-dehydrogenase 11.1.1.620.467
1m78NDPDihydrofolate reductase1.5.1.30.467
5dp2NAPCurF/0.464
1powFADPyruvate oxidase1.2.3.30.463
3giyFMN(S)-mandelate dehydrogenase1.1.99.310.463
3kjsNAPBifunctional dihydrofolate reductase-thymidylate synthase/0.463
3vt3VDXVitamin D3 receptor/0.463
4q71FADBifunctional protein PutA/0.463
3oibFDAPutative acyl-CoA dehydrogenase/0.462
4gh5NADShort-chain dehydrogenase/reductase SDR/0.462
2j2pSC2Ficolin-2/0.461
3dgaNDPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.461
3qlrNDPDihydrofolate reductase1.5.1.30.461
3irm1CYBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.460
3vrwYS5Vitamin D3 receptor/0.460
5eccNAPDehydrofolate reductase type I/0.460
5h8tRTLRetinol-binding protein 1/0.459
2nrySTUInterleukin-1 receptor-associated kinase 42.7.11.10.457
3vjoANPEpidermal growth factor receptor2.7.10.10.457
4hjoAQ4Epidermal growth factor receptor2.7.10.10.457
4kip1R9Mitogen-activated protein kinase 14/0.456
2nruT12Interleukin-1 receptor-associated kinase 42.7.11.10.455
2yxuATPPyridoxal kinase2.7.1.350.455
3w0aDS5Vitamin D3 receptor/0.455
4a99FADTetX family tetracycline inactivation enzyme/0.455
1drhNAPDihydrofolate reductase1.5.1.30.454
1j49NADD-lactate dehydrogenase1.1.1.280.454
4an4DUDPutative glycosyl transferase/0.454
4g2rH1LProbable propionyl-CoA carboxylase beta chain 66.4.1.30.454
4h1m0YJProtein-tyrosine kinase 2-beta2.7.10.20.454
5e8wSTUTGF-beta receptor type-12.7.11.300.454
1e6wNAD3-hydroxyacyl-CoA dehydrogenase type-21.1.1.350.453
4bf2STUMitogen-activated protein kinase kinase kinase 52.7.11.250.453
4xz3COAAcyl-CoA synthetase (NDP forming)/0.453
1kqwRTLCellular retinol-binding protein type II/0.452
1ur5NADMalate dehydrogenase/0.452
1y0s331Peroxisome proliferator-activated receptor delta/0.452
2aa0MTPAdenosine kinase2.7.1.200.452
2gr1FADFerredoxin reductase/0.452
2ix5FADAcyl-coenzyme A oxidase 4, peroxisomal1.3.3.60.451
3a783EVVitamin D3 receptor/0.451
3koo24DBifunctional epoxide hydrolase 23.3.2.100.451
4b1iA8PPoly(ADP-ribose) glycohydrolase3.2.1.1430.451
5hes032Mitogen-activated protein kinase kinase kinase 202.7.11.250.451
1b14NADAlcohol dehydrogenase1.1.1.10.450
1diuBDMDihydrofolate reductase1.5.1.30.450
1rx8FOLDihydrofolate reductase1.5.1.30.450
1sbyNADAlcohol dehydrogenase1.1.1.10.450
1xe55FEPlasmepsin-23.4.23.390.450
3rj5NADAlcohol dehydrogenase1.1.1.10.450
3w0yDS4Vitamin D3 receptor/0.450
4bc7FADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.450
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.449
4kl9NDPDihydrofolate reductase1.5.1.30.449
1bxsNADRetinal dehydrogenase 11.2.1.360.448
1crbRTLRetinol-binding protein 1/0.448
1uxjNADMalate dehydrogenase/0.448
3bv3P39Mitogen-activated protein kinase 14/0.448
3o3jBB4Peptide deformylase 1B, chloroplastic/mitochondrial3.5.1.880.448
1kfbIGPTryptophan synthase alpha chain/0.447
4cgfUJ6Integrase/0.447
4dc0NDPPutative ketoacyl reductase1.3.10.447
4u9zCOAAlpha-tubulin N-acetyltransferase 1/0.447
5iu4ZMAAdenosine receptor A2a/0.447
1fp2HMOIsoflavone-7-O-methyltransferase 82.1.1.1500.446
1ia1NDPDihydrofolate reductase1.5.1.30.446
2tpsTPSThiamine-phosphate synthase/0.446
3nxxNDPDihydrofolate reductase1.5.1.30.446
3uyk0CXProbable NDP-rhamnosyltransferase/0.446
5ez7FADProbable FAD-dependent oxidoreductase PA4991/0.446
5k2bZMAAdenosine receptor A2a/0.446
5k2dZMAAdenosine receptor A2a/0.446
1jpaANPEphrin type-B receptor 22.7.10.10.445
1rx1NAPDihydrofolate reductase1.5.1.30.445
1u1iNADMyo-inositol-1-phosphate synthase (Ino1)/0.445
3qd43Q63-phosphoinositide-dependent protein kinase 12.7.11.10.445
5iubCLRAdenosine receptor A2a/0.445
1b16NAQAlcohol dehydrogenase1.1.1.10.444
1n2sNAIdTDP-4-dehydrorhamnose reductase1.1.1.1330.444
2bbwGP5Adenylate kinase 4, mitochondrial/0.444
2vttLZDCyclin-dependent kinase 22.7.11.220.444
3k4nFADPyranose 2-oxidase/0.444
3oafOAGDihydrofolate reductase1.5.1.30.444
3w32W32Epidermal growth factor receptor2.7.10.10.444
3w33W19Epidermal growth factor receptor2.7.10.10.444
4bcrWY1Peroxisome proliferator-activated receptor alpha/0.444
4ewn0VRImidazole glycerol phosphate synthase subunit HisF4.1.30.444
4ure1PSCyclohexanol dehydrogenase/0.444
5jtbZMAAdenosine receptor A2a/0.444
1upcTPPN(2)-(2-carboxyethyl)arginine synthase/0.443
3poz03PEpidermal growth factor receptor2.7.10.10.443
4eiyZMAAdenosine receptor A2a/0.443
5hwrCOAHydroxymethylglutaryl-CoA synthase/0.443
2c31TZDOxalyl-CoA decarboxylase4.1.1.80.442
2fhnBNIAvidin-related protein 4/5/0.442
2hamC33Vitamin D3 receptor/0.442
2w6zL21Biotin carboxylase6.3.4.140.442
3rk507ZCyclin-dependent kinase 22.7.11.220.442
3up4FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.442
4a30QMIGlycylpeptide N-tetradecanoyltransferase/0.442
4qmySTUSerine/threonine-protein kinase 242.7.11.10.442
1dcyI3NPhospholipase A2, membrane associated/0.441
1tl7FOKAdenylate cyclase type 2/0.441
1tl7FOKAdenylate cyclase type 5/0.441
1y57MPZProto-oncogene tyrosine-protein kinase Src2.7.10.20.441
1y7lASN_LEU_ASN_ILECysteine synthase2.5.1.470.441
2ch6ADPN-acetyl-D-glucosamine kinase2.7.1.590.441
2nnlNAPDihydroflavonol 4-reductase1.1.1.2190.441
3bv7NAP3-oxo-5-beta-steroid 4-dehydrogenase/0.441
3qlsNDPDihydrofolate reductase1.5.1.30.441
3sw418KCyclin-dependent kinase 22.7.11.220.441
3vt5YI2Vitamin D3 receptor/0.441
4hbgNDP3-oxoacyl-[acyl-carrier-protein] reductase1.1.1.1000.441
1fm4DXCMajor pollen allergen Bet v 1-L/0.440
2bxqIMNSerum albumin/0.440
2wxvWXVCyclin-dependent kinase 22.7.11.220.440
3ac3KSHTyrosine-protein kinase Lck2.7.10.20.440
3lqfNADGalactitol dehydrogenase/0.440
3unj0BXCyclin-dependent kinase 22.7.11.220.440
3w0jT08Vitamin D3 receptor/0.440
4cukNAID-lactate dehydrogenase/0.440