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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
3rs4GNPGTPase HRas

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
3rs4GNPGTPase HRas/1.000
4dltGNPGTPase HRas/0.865
3lbhGNPGTPase HRas/0.840
3lbiGNPGTPase HRas/0.835
3lbnGNPGTPase HRas/0.778
3k8yGNPGTPase HRas/0.704
4g0nGNPGTPase HRas/0.693
4l9wGNPGTPase HRas/0.693
3rslGNPGTPase HRas/0.689
3rs0GNPGTPase HRas/0.685
4dlwGNPGTPase HRas/0.675
4dsnGCPGTPase KRas/0.673
3l8yGNPGTPase HRas/0.670
2rgeGNPGTPase HRas/0.669
3rs7GNPGTPase HRas/0.669
3oiwGNPGTPase HRas/0.662
3pitGNPRas-related protein M-Ras/0.662
4dlzGNPGTPase HRas/0.658
3kkoGNPRas-related protein M-Ras/0.653
3i3sGNPGTPase HRas/0.652
2rgcGNPGTPase HRas/0.651
5dhaGNPGTP-binding nuclear protein Ran/0.650
2c5lGTPGTPase HRas/0.649
5difGNPGTP-binding nuclear protein Ran/0.642
2qmeGCPRas-related C3 botulinum toxin substrate 3/0.640
4rkfGNPRas-related protein Rab-3/0.640
3ddcGNPGTPase HRas/0.639
5b2zGNPGTPase HRas/0.638
4dlsGNPGTPase HRas/0.633
3x1zGNPRas-related protein Rap-1b/0.629
4hdoGNPRas-related protein Rap-1b/0.625
1g17GNPRas-related protein SEC4/0.624
3v4fGNPGTPase HRas/0.622
3a58GNPGTP-binding protein RHO1/0.618
2rgbGNPGTPase HRas/0.617
3kudGDPGTPase HRas/0.617
4nyjGNPGTPase HRas/0.616
3oiuGNPGTPase HRas/0.615
1e96GTPRas-related C3 botulinum toxin substrate 1/0.612
1ibrGNPGTP-binding nuclear protein Ran/0.612
1t91GTPRas-related protein Rab-7a/0.611
3a6pGTPGTP-binding nuclear protein Ran/0.611
4l9sGDPGTPase HRas/0.609
4nyiGNPGTPase HRas/0.607
1yzqGNPRas-related protein Rab-6A/0.604
4qxaGTPRas-related protein Rab-9A/0.601
4lhwGNPRas-related protein Rab-8A/0.600
5jljGNPGTP-binding nuclear protein Ran/0.599
3sbdGNPRas-related C3 botulinum toxin substrate 1/0.597
4tq9GDPGTPase KRas/0.597
3e5hGNPRas-related protein Rab-28/0.593
4dlxGNPGTPase HRas/0.592
2bkuGTPGTP-binding nuclear protein Ran/0.589
4lv6GDPGTPase KRas/0.587
1mh1GNPRas-related C3 botulinum toxin substrate 1/0.586
4hdqGNPRas-related protein Rap-1b/0.585
1xtsGTPGTP-binding protein Rheb/0.584
3w3zGTPGTP-binding nuclear protein Ran/0.584
4lpkGDPGTPase KRas/0.584
3tgpGNPGTPase HRas/0.583
4l8gGDPGTPase KRas/0.582
4mitGTPRho-related protein racC/0.582
1a2bGSPTransforming protein RhoA/0.579
1kmqGNPTransforming protein RhoA/0.577
3ea5GDPGTP-binding nuclear protein Ran/0.577
3tsoGNPRas-related protein Rab-25/0.576
4epwGDPGTPase KRas/0.574
1zc4GNPRas-related protein Ral-A/0.573
3rabGNPRas-related protein Rab-3A/0.572
2ce2GDPGTPase HRas/0.571
4wa7GDPGTPase KRas/0.571
1xtrGNPGTP-binding protein Rheb/0.570
3kkqGDPRas-related protein M-Ras/0.570
4dlvGNPGTPase HRas/0.570
1zbdGTPRas-related protein Rab-3A/0.567
2gcpGSPRho-related GTP-binding protein RhoC/0.567
1cxzGSPTransforming protein RhoA/0.565
1zd9GDPADP-ribosylation factor-like protein 8A/0.565
4o2lGTPGTP-binding protein Rheb/0.564
2fe4GDPRas-related protein Rab-6B/0.562
3oesGNPGTPase RhebL1/0.562
4dsoGSPGTPase KRas/0.561
3bbpGTPRas-related protein Rab-6A/0.559
4q03GDPGTPase KRas/0.559
1vg8GNPRas-related protein Rab-7a/0.558
1zc3GNPRas-related protein Ral-A/0.558
4o2rGDPGTP-binding protein Rheb/0.557
4obeGDPGTPase KRas/0.556
2ov2GCPRas-related C3 botulinum toxin substrate 3/0.555
3th5GNPRas-related C3 botulinum toxin substrate 1/0.555
3wyfGTPGTP-binding nuclear protein/0.555
4lrwGDPGTPase KRas/0.554
2fjuGSPRas-related C3 botulinum toxin substrate 1/0.552
1yu9GNPRas-related protein Rab-4A/0.551
4epxGDPGTPase KRas/0.548
4o25GTPGTP-binding protein Rheb/0.548
3rs5GNPGTPase HRas/0.547
4kvgGTPRas-related protein Rap-1A/0.546
1x1rGDPRas-related protein M-Ras/0.544
3sbeGNPRas-related C3 botulinum toxin substrate 1/0.543
3k9lGNPGTPase HRas/0.542
3nbzGTPGTP-binding nuclear protein Ran/0.542
3x1wGDPRas-related protein Rap-1b/0.542
4q02GDPGTPase KRas/0.540
2ffqGSPRas-related protein Rab-6B/0.539
3oivGNPGTPase HRas/0.539
1d5cGDPGTPase (Rab6)/0.535
1yhnGTPRas-related protein Rab-7a/0.533
4ql3GDPGTPase KRas/0.533
1z0dGDPRas-related protein Rab-5C/0.532
4xvqGNPGTPase HRas/0.530
1z2aGDPRas-related protein Rab-23/0.527
3kz1GSPTransforming protein RhoA/0.526
1n6lGTPRas-related protein Rab-5A/0.525
4js0GNPCell division control protein 42 homolog/0.525
4uj3GNPRas-related protein Rab-11A/0.525
2fg5GNPRas-related protein Rab-31/0.524
2p2lGDPRas-related C3 botulinum toxin substrate 1/0.524
3kucGDPRas-related protein Rap-1A/0.524
4ldjGDPGTPase KRas/0.523
2mscGDPMHC class I alpha chain/0.521
4xvrGNPGTPase HRas/0.521
2bmeGNPRas-related protein Rab-4A/0.519
1k5dGNPGTP-binding nuclear protein Ran/0.518
3bc1GNPRas-related protein Rab-27A/0.517
2msdGNPMHC class I alpha chain/0.515
2rggGNPGTPase HRas/0.514
1m7bGTPRho-related GTP-binding protein RhoE/0.512
1lfdGNPGTPase HRas/0.510
1ow3GDPTransforming protein RhoA/0.510
1oixGDPRas-related protein Rab-11A/0.508
4dsuGDPGTPase KRas/0.507
4dxaGSPRas-related protein Rap-1b/0.507
4gzlGNPRas-related C3 botulinum toxin substrate 1/0.504
3qbtGNPRas-related protein Rab-8A/0.503
3eg5GNPCell division control protein 42 homolog/0.502
2cl6CAGGTPase HRas/0.501
4cidANPEH domain-containing protein 2/0.500
4ol0GTPGTP-binding nuclear protein Ran/0.499
4g2i0VQVitamin D3 receptor/0.498
1gwnGTPRho-related GTP-binding protein RhoE/0.496
3umsGDPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.495
1z2cGNPRho-related GTP-binding protein RhoC/0.494
2q3fGNPRas-related GTP-binding protein D/0.488
3cphGDPRas-related protein SEC4/0.485
2a9z26AAdenosine kinase2.7.1.200.484
5hpyGDPTransforming protein RhoA/0.483
2j0vGDPRac-like GTP-binding protein ARAC7/0.482
2o4jVD4Vitamin D3 receptor/0.482
2mseGNPMHC class I alpha chain/0.478
3vhxGTPADP-ribosylation factor 6/0.476
4panGDPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.475
3tklGTPRas-related protein Rab-1A/0.474
2o4rVD5Vitamin D3 receptor/0.472
4lzwTHMUridine phosphorylase/0.472
2zlcVDXVitamin D3 receptor/0.471
2g0nGDPRas-related C3 botulinum toxin substrate 3/0.470
2hb8MVDVitamin D3 receptor/0.470
2a9y26AAdenosine kinase2.7.1.200.469
1q4wDQUQueuine tRNA-ribosyltransferase2.4.2.290.468
2ic5GDPRas-related C3 botulinum toxin substrate 3/0.468
4ead0NPThymidine phosphorylase2.4.2.40.468
1g16GDPRas-related protein SEC4/0.467
1giaGSPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.467
1v8kANPKinesin-like protein KIF2C/0.465
2abjCBCBranched-chain-amino-acid aminotransferase, cytosolic2.6.1.420.465
1uadGNPRas-related protein Ral-A/0.464
2harOCCVitamin D3 receptor/0.464
4mv3ACPBiotin carboxylase6.3.4.140.464
4uj5GNPRas-related protein Rab-11A/0.464
2ji9TPWOxalyl-CoA decarboxylase4.1.1.80.461
4edz0O5Hematopoietic prostaglandin D synthase/0.460
4q0a4OAVitamin D3 receptor A/0.460
4qzuRTLRetinol-binding protein 2/0.460
1db1VDXVitamin D3 receptor/0.459
1culGSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.458
4iteTEYVitamin D3 receptor/0.457
2bxqIMNSerum albumin/0.455
3w0aDS5Vitamin D3 receptor/0.455
1wdtGTPElongation factor G (EF-G-2)/0.454
2clsGTPRho-related GTP-binding protein Rho6/0.454
2wu2CBESuccinate dehydrogenase iron-sulfur subunit1.3.5.10.454
2wu2CBESuccinate dehydrogenase cytochrome b556 subunit/0.454
3gy9COAGCN5-related N-acetyltransferase/0.454
3nn6HNK6-hydroxy-L-nicotine oxidase/0.454
4ai8DZAHypoxia-inducible factor 1-alpha inhibitor1.14.11.300.454
4paoGSPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.454
1kqwRTLCellular retinol-binding protein type II/0.453
1m2oGNPSmall COPII coat GTPase SAR13.6.50.453
1txiTX5Vitamin D3 receptor/0.453
1vhnFMNtRNA-dihydrouridine synthase/0.453
2yloTESAndrogen receptor/0.453
3gyaCOAGCN5-related N-acetyltransferase/0.453
3w0c6DSVitamin D3 receptor/0.453
4mv1ADPBiotin carboxylase6.3.4.140.452
1ky2GNPGTP-binding protein YPT7/0.451
1rt9IMHPurine nucleoside phosphorylase2.4.2.10.451
2p1u4TNRetinoic acid receptor RXR-alpha/0.451
3refGDPRho family GTPase/0.451
4bfwZVWPantothenate kinase2.7.1.330.451
4dvi2IWTankyrase-12.4.2.300.451
4k5o1OTM1 family aminopeptidase3.4.110.451
4lb2DM5Serum albumin/0.451
1s0zEB1Vitamin D3 receptor/0.450
2gvdFKPAdenylate cyclase type 2/0.450
2gvdFKPAdenylate cyclase type 5/0.450
2ociTYCValacyclovir hydrolase3.10.450
4j531J4Serine/threonine-protein kinase PLK12.7.11.210.450
1g2vTTPGlucose-1-phosphate thymidylyltransferase/0.449
1towCRZFatty acid-binding protein, adipocyte/0.449
2wnsOMPUridine 5'-monophosphate synthase2.4.2.100.449
2wu5CBESuccinate dehydrogenase iron-sulfur subunit1.3.5.10.449
2wu5CBESuccinate dehydrogenase cytochrome b556 subunit/0.449
3m7rVDXVitamin D3 receptor/0.449
3r9xGNPGTPase Era/0.449
3tl1JROPutative polyketide cyclase/0.449
4fhi0S4Vitamin D3 receptor A/0.449
4obuPLPPyridoxal-dependent decarboxylase domain protein/0.449
4xybNDPFormate dehydrogenase/0.449
2vczVC3Hematopoietic prostaglandin D synthase/0.448
2x06NADL-sulfolactate dehydrogenase/0.448
2ydd2AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.448
4xymCOAAcyl-CoA synthetase (NDP forming)/0.448
1pwyAC2Purine nucleoside phosphorylase2.4.2.10.447
1ro98BRcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.447
1tkaN3TTransketolase 12.2.1.10.447
3dh8B4NUncharacterized protein PA1000/0.447
3k7mFAD6-hydroxy-L-nicotine oxidase/0.447
4bn1ADPAurora kinase A2.7.11.10.447
4fgcPQ0NADPH-dependent 7-cyano-7-deazaguanine reductase1.7.1.130.447
1aztGSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.446
2dy9ADPNucleoside diphosphate kinase2.7.4.60.446
2oegUPGUDP-glucose pyrophosphorylase/0.446
3b9lAZZSerum albumin/0.446
3c0i3AMPeripheral plasma membrane protein CASK2.7.11.10.446
4c6uTLG3-oxoacyl-ACP synthase/0.446
4itfTFYVitamin D3 receptor/0.446
4m8e29VRetinoic acid receptor RXR-alpha/0.446
1bcpATPPertussis toxin subunit 4/0.445
1bcpATPPertussis toxin subunit 5/0.445
1f3eDPZQueuine tRNA-ribosyltransferase2.4.2.290.445
1z7yAA5Cysteine synthase 12.5.1.470.445
2r6jNDPEugenol synthase 11.1.1.3180.445
4g0k0VSGlutathionyl-hydroquinone reductase YqjG1.80.445
1s19MC9Vitamin D3 receptor/0.444
2dw4FADLysine-specific histone demethylase 1A10.444
3hpqAP5Adenylate kinase/0.444
4gzmGSPRas-related C3 botulinum toxin substrate 1/0.444
4rr7A3SProbable threonine--tRNA ligase 26.1.1.30.444
2hb7O1CVitamin D3 receptor/0.443
3k4s0MOcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.443
4azwATPO-antigen chain terminator bifunctional methyltransferase/kinase WbdD/0.443
4cf7ADPAdenylate kinase/0.443
4fhd0TTSpore photoproduct lyase/0.443
1qyw5SDEstradiol 17-beta-dehydrogenase 11.1.1.620.442
1t65DHTAndrogen receptor/0.442
2rqfJH3Hemolymph juvenile hormone binding protein/0.442
2vigFADShort-chain specific acyl-CoA dehydrogenase, mitochondrial1.3.8.10.442
3kxoKXOHematopoietic prostaglandin D synthase/0.442
3maaFKPAdenylate cyclase type 2/0.442
3maaFKPAdenylate cyclase type 5/0.442
3sfxJANUncharacterized protein/0.442
3t3q9PLCytochrome P450 2A61.14.130.442
3vt5YI2Vitamin D3 receptor/0.442
4dzzADPPlasmid partitioning protein ParF/0.442
4wuoNAD3-isopropylmalate dehydrogenase1.1.1.850.442
5e8jSAHmRNA cap guanine-N7 methyltransferase2.1.1.560.442
5iqdGNPBifunctional AAC/APH2.3.10.442
5kf1COAPredicted acetyltransferase/0.442
1toiHCIAspartate aminotransferase2.6.1.10.441
2ic5GNPRas-related C3 botulinum toxin substrate 3/0.441
3c16GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.441
1ve3SAMUncharacterized protein/0.440
2aa2AS4Mineralocorticoid receptor/0.440
2xvv9DNSerum albumin/0.440
3up0D7SaceDAF-12/0.440
3w5tLHPVitamin D3 receptor/0.440
3x025GPPhosphatidylinositol 5-phosphate 4-kinase type-2 beta2.7.1.1490.440
4gojGNPADP-ribosylation factor-like protein 3/0.440
4pl9ADPEthylene receptor 1/0.440
5iqiGNPBifunctional AAC/APH2.3.10.440