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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
3l8yGNPGTPase HRas

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
3l8yGNPGTPase HRas/1.000
5b2zGNPGTPase HRas/0.829
3i3sGNPGTPase HRas/0.733
3v4fGNPGTPase HRas/0.671
3oiwGNPGTPase HRas/0.658
3lbnGNPGTPase HRas/0.654
3rs5GNPGTPase HRas/0.654
4dlzGNPGTPase HRas/0.647
3rslGNPGTPase HRas/0.646
3oiuGNPGTPase HRas/0.645
2rgbGNPGTPase HRas/0.644
3kkoGNPRas-related protein M-Ras/0.644
3ddcGNPGTPase HRas/0.642
3rs7GNPGTPase HRas/0.640
4g0nGNPGTPase HRas/0.639
3pitGNPRas-related protein M-Ras/0.638
2c5lGTPGTPase HRas/0.635
3e5hGNPRas-related protein Rab-28/0.635
3rs4GNPGTPase HRas/0.635
3lbiGNPGTPase HRas/0.634
4dltGNPGTPase HRas/0.634
4k81GTPGTPase HRas/0.630
2rgcGNPGTPase HRas/0.629
2rgeGNPGTPase HRas/0.629
3x1zGNPRas-related protein Rap-1b/0.629
4dlxGNPGTPase HRas/0.629
3oivGNPGTPase HRas/0.626
4nyjGNPGTPase HRas/0.625
1t91GTPRas-related protein Rab-7a/0.623
4dsnGCPGTPase KRas/0.622
3rs0GNPGTPase HRas/0.619
3kucGDPRas-related protein Rap-1A/0.618
1zbdGTPRas-related protein Rab-3A/0.617
2gilGTPRas-related protein Rab-6A/0.615
4dlsGNPGTPase HRas/0.615
3kudGDPGTPase HRas/0.614
4hdoGNPRas-related protein Rap-1b/0.612
1xtsGTPGTP-binding protein Rheb/0.610
4nyiGNPGTPase HRas/0.610
1g17GNPRas-related protein SEC4/0.609
3lbhGNPGTPase HRas/0.609
4dlwGNPGTPase HRas/0.608
1zd9GDPADP-ribosylation factor-like protein 8A/0.607
3a6pGTPGTP-binding nuclear protein Ran/0.605
1e96GTPRas-related C3 botulinum toxin substrate 1/0.604
3w3zGTPGTP-binding nuclear protein Ran/0.599
3rabGNPRas-related protein Rab-3A/0.598
4lhwGNPRas-related protein Rab-8A/0.597
5dhaGNPGTP-binding nuclear protein Ran/0.597
5difGNPGTP-binding nuclear protein Ran/0.596
4tq9GDPGTPase KRas/0.595
2qmeGCPRas-related C3 botulinum toxin substrate 3/0.593
4dlvGNPGTPase HRas/0.593
4l9wGNPGTPase HRas/0.592
4qxaGTPRas-related protein Rab-9A/0.592
4rkfGNPRas-related protein Rab-3/0.587
3k8yGNPGTPase HRas/0.586
3ea5GDPGTP-binding nuclear protein Ran/0.584
3oesGNPGTPase RhebL1/0.582
4kvgGTPRas-related protein Rap-1A/0.582
1yzqGNPRas-related protein Rab-6A/0.579
3sbdGNPRas-related C3 botulinum toxin substrate 1/0.578
1ibrGNPGTP-binding nuclear protein Ran/0.577
1zc3GNPRas-related protein Ral-A/0.576
2x19GTPGTP-binding nuclear protein GSP1/CNR1/0.574
3bbpGTPRas-related protein Rab-6A/0.574
2zetGTPRas-related protein Rab-27B/0.573
4mitGTPRho-related protein racC/0.573
3a58GNPGTP-binding protein RHO1/0.570
4l9sGDPGTPase HRas/0.570
4o25GTPGTP-binding protein Rheb/0.569
3nbzGTPGTP-binding nuclear protein Ran/0.568
4q03GDPGTPase KRas/0.563
1xtrGNPGTP-binding protein Rheb/0.562
2fe4GDPRas-related protein Rab-6B/0.562
5jljGNPGTP-binding nuclear protein Ran/0.562
4obeGDPGTPase KRas/0.561
1zc4GNPRas-related protein Ral-A/0.560
4ql3GDPGTPase KRas/0.560
4epxGDPGTPase KRas/0.559
3lawGNPRas-related protein Rab-7a/0.557
4xvrGNPGTPase HRas/0.556
1kmqGNPTransforming protein RhoA/0.555
3tsoGNPRas-related protein Rab-25/0.554
1yhnGTPRas-related protein Rab-7a/0.553
2ce2GDPGTPase HRas/0.551
3tnfGNPRas-related protein Rab-8A/0.550
4dsoGSPGTPase KRas/0.550
3sbeGNPRas-related C3 botulinum toxin substrate 1/0.549
1lfdGNPGTPase HRas/0.548
2rggGNPGTPase HRas/0.547
2bkuGTPGTP-binding nuclear protein Ran/0.546
2fjuGSPRas-related C3 botulinum toxin substrate 1/0.546
3qbtGNPRas-related protein Rab-8A/0.546
4lpkGDPGTPase KRas/0.546
1yu9GNPRas-related protein Rab-4A/0.544
4ol0GTPGTP-binding nuclear protein Ran/0.542
1cxzGSPTransforming protein RhoA/0.541
1m7bGTPRho-related GTP-binding protein RhoE/0.541
4hdqGNPRas-related protein Rap-1b/0.540
1a2bGSPTransforming protein RhoA/0.537
2gcpGSPRho-related GTP-binding protein RhoC/0.537
2ffqGSPRas-related protein Rab-6B/0.535
4lucGDPGTPase KRas/0.535
4o2rGDPGTP-binding protein Rheb/0.535
4epwGDPGTPase KRas/0.534
4q02GDPGTPase KRas/0.533
1d5cGDPGTPase (Rab6)/0.532
1oixGDPRas-related protein Rab-11A/0.531
3cphGDPRas-related protein SEC4/0.531
1n6lGTPRas-related protein Rab-5A/0.530
4dxaGSPRas-related protein Rap-1b/0.530
4l8gGDPGTPase KRas/0.530
4o2lGTPGTP-binding protein Rheb/0.529
1mh1GNPRas-related C3 botulinum toxin substrate 1/0.528
1s1cGNPTransforming protein RhoA/0.528
1vg8GNPRas-related protein Rab-7a/0.528
3bc1GNPRas-related protein Rab-27A/0.528
4wa7GDPGTPase KRas/0.527
3wyfGTPGTP-binding nuclear protein/0.526
3k9lGNPGTPase HRas/0.523
3kkqGDPRas-related protein M-Ras/0.523
4uj3GNPRas-related protein Rab-11A/0.522
1ow3GDPTransforming protein RhoA/0.521
4lv6GDPGTPase KRas/0.521
3mjhGTPRas-related protein Rab-5A/0.519
2w2xGSPRas-related C3 botulinum toxin substrate 2/0.518
2msdGNPMHC class I alpha chain/0.517
3tgpGNPGTPase HRas/0.516
2ov2GCPRas-related C3 botulinum toxin substrate 3/0.515
3th5GNPRas-related C3 botulinum toxin substrate 1/0.515
1x1rGDPRas-related protein M-Ras/0.514
4dsuGDPGTPase KRas/0.514
1g16GDPRas-related protein SEC4/0.513
1k5dGNPGTP-binding nuclear protein Ran/0.512
3kz1GSPTransforming protein RhoA/0.512
4js0GNPCell division control protein 42 homolog/0.510
2clsGTPRho-related GTP-binding protein Rho6/0.509
3tklGTPRas-related protein Rab-1A/0.508
4lrwGDPGTPase KRas/0.508
4ldjGDPGTPase KRas/0.506
3eg5GNPCell division control protein 42 homolog/0.505
4xoiGTPTransforming protein RhoA/0.504
4xvqGNPGTPase HRas/0.503
1z2aGDPRas-related protein Rab-23/0.502
3wygGTPGTP-binding nuclear protein GSP1/CNR1/0.500
2xtzGSPGuanine nucleotide-binding protein alpha-1 subunit/0.498
4cymGCPRas-related protein Rab-32/0.497
2cl6CAGGTPase HRas/0.492
1uadGNPRas-related protein Ral-A/0.487
3x1wGDPRas-related protein Rap-1b/0.486
1z0aGDPRas-related protein Rab-2A/0.485
2ic5GNPRas-related C3 botulinum toxin substrate 3/0.485
4uj5GNPRas-related protein Rab-11A/0.485
5c46GSPRas-related protein Rab-11A/0.485
2bmeGNPRas-related protein Rab-4A/0.484
1gwnGTPRho-related GTP-binding protein RhoE/0.480
2p2lGDPRas-related C3 botulinum toxin substrate 1/0.480
4cidANPEH domain-containing protein 2/0.475
5hpyGDPTransforming protein RhoA/0.473
2mscGDPMHC class I alpha chain/0.470
2hb8MVDVitamin D3 receptor/0.468
3w0c6DSVitamin D3 receptor/0.467
2fg5GNPRas-related protein Rab-31/0.466
4gzlGNPRas-related C3 botulinum toxin substrate 1/0.464
1tu3GNPRas-related protein Rab-5A/0.463
4q0a4OAVitamin D3 receptor A/0.463
1z2cGNPRho-related GTP-binding protein RhoC/0.462
2j5xGSPADP-ribosylation factor 6/0.461
3w0aDS5Vitamin D3 receptor/0.461
4wda2AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.461
3t1tGDPProbable gliding protein mglA/0.459
4ead0NPThymidine phosphorylase2.4.2.40.459
3a783EVVitamin D3 receptor/0.458
2mseGNPMHC class I alpha chain/0.457
3da24MDCarbonic anhydrase 134.2.1.10.457
4ycpFMNtRNA-dihydrouridine(16) synthase/0.457
2rdn1PL1-deoxypentalenic acid 11-beta-hydroxylase1.14.11.350.456
1obnASVIsopenicillin N synthase1.21.3.10.455
2zlcVDXVitamin D3 receptor/0.455
1ky2GNPGTP-binding protein YPT7/0.454
3umsGDPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.454
2d3aADPGlutamine synthetase root isozyme 36.3.1.20.453
2gvdFKPAdenylate cyclase type 2/0.453
2gvdFKPAdenylate cyclase type 5/0.453
3pqbVGPPutative oxidoreductase/0.453
1rzuADPGlycogen synthase 12.4.1.210.451
2q3fGNPRas-related GTP-binding protein D/0.451
5ab6CAANonspecific lipid-transfer protein, putative/0.451
4ihjGTPTubulin alpha-1B chain/0.450
4wdb2AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.450
5c1mCLRMu-type opioid receptor/0.450
2a9y26AAdenosine kinase2.7.1.200.449
2zl9VDAVitamin D3 receptor/0.449
3c14FOKAdenylate cyclase type 2/0.449
3c14FOKAdenylate cyclase type 5/0.449
1db1VDXVitamin D3 receptor/0.448
2g0nGDPRas-related C3 botulinum toxin substrate 3/0.448
4g2i0VQVitamin D3 receptor/0.448
1ay0TPPTransketolase 12.2.1.10.447
1z0dGDPRas-related protein Rab-5C/0.447
2hamC33Vitamin D3 receptor/0.447
5iqbGNPBifunctional AAC/APH2.3.10.447
2fghATPGelsolin/0.446
3naxMP73-phosphoinositide-dependent protein kinase 12.7.11.10.446
1fmjRTLRetinol dehydratase/0.445
4wbnGTPTubulin alpha-1B chain/0.445
4zzi1NSNAD-dependent protein deacetylase sirtuin-13.5.10.445
1e0jANPDNA primase/helicase2.7.70.444
1s19MC9Vitamin D3 receptor/0.444
3k7mFAD6-hydroxy-L-nicotine oxidase/0.444
4rriA3TProbable threonine--tRNA ligase 26.1.1.30.444
2hc4VDXVitamin D3 receptor A/0.443
3e32ED2Protein farnesyltransferase subunit beta2.5.1.580.443
3hdyGDUUDP-galactopyranose mutase/0.443
3pzcCOAAmino acid--[acyl-carrier-protein] ligase 16.2.1.n20.443
4k5o1OTM1 family aminopeptidase3.4.110.443
3adaNADSubunit alpha of sarocosine oxidase/0.442
3gmd2M3Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.442
3q9bB3NAcetylpolyamine amidohydrolase/0.442
3sqxANPATP-dependent RNA helicase MSS116, mitochondrial3.6.4.130.442
3vt9YI4Vitamin D3 receptor/0.442
4g20484Vitamin D3 receptor A/0.442
4iteTEYVitamin D3 receptor/0.442
1txiTX5Vitamin D3 receptor/0.441
2xauADPPre-mRNA-splicing factor ATP-dependent RNA helicase PRP433.6.4.130.441
2y8lADP5'-AMP-activated protein kinase subunit gamma-1/0.441
2fhjMFNFormylmethanofuran--tetrahydromethanopterin formyltransferase2.3.1.1010.440
3v2uATPProtein GAL3/0.440
4lb2DM5Serum albumin/0.440
5iqaGNPBifunctional AAC/APH2.3.10.440