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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
4l9wGNPGTPase HRas

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
4l9wGNPGTPase HRas/1.000
4dlzGNPGTPase HRas/0.706
3rs4GNPGTPase HRas/0.705
4dlxGNPGTPase HRas/0.701
2rgbGNPGTPase HRas/0.696
3lbnGNPGTPase HRas/0.693
3rslGNPGTPase HRas/0.690
3rs0GNPGTPase HRas/0.679
4dlsGNPGTPase HRas/0.677
4dlvGNPGTPase HRas/0.676
3lbiGNPGTPase HRas/0.674
3rs7GNPGTPase HRas/0.674
2rgcGNPGTPase HRas/0.672
3l8yGNPGTPase HRas/0.672
4dltGNPGTPase HRas/0.670
3v4fGNPGTPase HRas/0.667
2rgeGNPGTPase HRas/0.658
3oivGNPGTPase HRas/0.655
4dsnGCPGTPase KRas/0.654
3pitGNPRas-related protein M-Ras/0.653
4dlwGNPGTPase HRas/0.652
3rs5GNPGTPase HRas/0.651
3oiwGNPGTPase HRas/0.649
2c5lGTPGTPase HRas/0.648
3lbhGNPGTPase HRas/0.646
1g17GNPRas-related protein SEC4/0.645
4g0nGNPGTPase HRas/0.645
5b2zGNPGTPase HRas/0.645
3kudGDPGTPase HRas/0.638
5difGNPGTP-binding nuclear protein Ran/0.636
3i3sGNPGTPase HRas/0.633
3k8yGNPGTPase HRas/0.633
1e96GTPRas-related C3 botulinum toxin substrate 1/0.632
3e5hGNPRas-related protein Rab-28/0.629
4hdoGNPRas-related protein Rap-1b/0.627
4k81GTPGTPase HRas/0.626
3kkoGNPRas-related protein M-Ras/0.625
3a6pGTPGTP-binding nuclear protein Ran/0.622
3oiuGNPGTPase HRas/0.621
3ddcGNPGTPase HRas/0.619
4nyiGNPGTPase HRas/0.619
4lhwGNPRas-related protein Rab-8A/0.618
5dhaGNPGTP-binding nuclear protein Ran/0.618
3a58GNPGTP-binding protein RHO1/0.617
4rkfGNPRas-related protein Rab-3/0.617
3kucGDPRas-related protein Rap-1A/0.616
4dsoGSPGTPase KRas/0.616
1zbdGTPRas-related protein Rab-3A/0.613
4nyjGNPGTPase HRas/0.607
3sbdGNPRas-related C3 botulinum toxin substrate 1/0.605
4lpkGDPGTPase KRas/0.605
3rabGNPRas-related protein Rab-3A/0.604
5jljGNPGTP-binding nuclear protein Ran/0.604
3x1zGNPRas-related protein Rap-1b/0.602
4lrwGDPGTPase KRas/0.602
3w3zGTPGTP-binding nuclear protein Ran/0.598
1t91GTPRas-related protein Rab-7a/0.594
3ea5GDPGTP-binding nuclear protein Ran/0.590
4l8gGDPGTPase KRas/0.586
1xtsGTPGTP-binding protein Rheb/0.585
1zc4GNPRas-related protein Ral-A/0.584
4mitGTPRho-related protein racC/0.581
1ibrGNPGTP-binding nuclear protein Ran/0.579
2bkuGTPGTP-binding nuclear protein Ran/0.578
2fe4GDPRas-related protein Rab-6B/0.577
1zc3GNPRas-related protein Ral-A/0.573
4hdqGNPRas-related protein Rap-1b/0.573
1zd9GDPADP-ribosylation factor-like protein 8A/0.572
4kvgGTPRas-related protein Rap-1A/0.572
4l9sGDPGTPase HRas/0.571
4lv6GDPGTPase KRas/0.571
3bbpGTPRas-related protein Rab-6A/0.570
4tq9GDPGTPase KRas/0.570
1cxzGSPTransforming protein RhoA/0.569
4o25GTPGTP-binding protein Rheb/0.569
2gilGTPRas-related protein Rab-6A/0.567
1yzqGNPRas-related protein Rab-6A/0.562
2zetGTPRas-related protein Rab-27B/0.560
1kmqGNPTransforming protein RhoA/0.558
2fjuGSPRas-related C3 botulinum toxin substrate 1/0.556
3tnfGNPRas-related protein Rab-8A/0.553
4epxGDPGTPase KRas/0.552
3tsoGNPRas-related protein Rab-25/0.550
3wygGTPGTP-binding nuclear protein GSP1/CNR1/0.550
4obeGDPGTPase KRas/0.550
2qmeGCPRas-related C3 botulinum toxin substrate 3/0.546
1vg8GNPRas-related protein Rab-7a/0.545
2rggGNPGTPase HRas/0.544
1a2bGSPTransforming protein RhoA/0.543
1k5dGNPGTP-binding nuclear protein Ran/0.542
1m7bGTPRho-related GTP-binding protein RhoE/0.542
3bc1GNPRas-related protein Rab-27A/0.542
3kkqGDPRas-related protein M-Ras/0.542
3x1wGDPRas-related protein Rap-1b/0.542
3wyfGTPGTP-binding nuclear protein/0.540
4ol0GTPGTP-binding nuclear protein Ran/0.540
1xtrGNPGTP-binding protein Rheb/0.538
2ffqGSPRas-related protein Rab-6B/0.538
3tgpGNPGTPase HRas/0.538
4epwGDPGTPase KRas/0.537
4o2lGTPGTP-binding protein Rheb/0.537
2x19GTPGTP-binding nuclear protein GSP1/CNR1/0.536
4q02GDPGTPase KRas/0.536
4xvqGNPGTPase HRas/0.536
3sbeGNPRas-related C3 botulinum toxin substrate 1/0.535
4ql3GDPGTPase KRas/0.534
4qxaGTPRas-related protein Rab-9A/0.532
1s1cGNPTransforming protein RhoA/0.530
2gcpGSPRho-related GTP-binding protein RhoC/0.530
1yhnGTPRas-related protein Rab-7a/0.528
1z0dGDPRas-related protein Rab-5C/0.528
1x1rGDPRas-related protein M-Ras/0.524
2ce2GDPGTPase HRas/0.524
4q03GDPGTPase KRas/0.523
4gzlGNPRas-related C3 botulinum toxin substrate 1/0.521
4xvrGNPGTPase HRas/0.521
2ov2GCPRas-related C3 botulinum toxin substrate 3/0.520
1lfdGNPGTPase HRas/0.519
1n6lGTPRas-related protein Rab-5A/0.519
1z2aGDPRas-related protein Rab-23/0.519
3k9lGNPGTPase HRas/0.519
4wa7GDPGTPase KRas/0.519
2p2lGDPRas-related C3 botulinum toxin substrate 1/0.518
2w2xGSPRas-related C3 botulinum toxin substrate 2/0.517
1mh1GNPRas-related C3 botulinum toxin substrate 1/0.516
4ldjGDPGTPase KRas/0.515
3qbtGNPRas-related protein Rab-8A/0.514
3kz1GSPTransforming protein RhoA/0.512
3lawGNPRas-related protein Rab-7a/0.512
3th5GNPRas-related C3 botulinum toxin substrate 1/0.512
4dsuGDPGTPase KRas/0.512
2msdGNPMHC class I alpha chain/0.510
4js0GNPCell division control protein 42 homolog/0.510
2fg5GNPRas-related protein Rab-31/0.509
1gwnGTPRho-related GTP-binding protein RhoE/0.508
4lucGDPGTPase KRas/0.508
1ow3GDPTransforming protein RhoA/0.507
2mscGDPMHC class I alpha chain/0.507
1z2cGNPRho-related GTP-binding protein RhoC/0.506
1d5cGDPGTPase (Rab6)/0.503
4uj3GNPRas-related protein Rab-11A/0.502
1oixGDPRas-related protein Rab-11A/0.501
1yu9GNPRas-related protein Rab-4A/0.501
3nbzGTPGTP-binding nuclear protein Ran/0.501
1z0aGDPRas-related protein Rab-2A/0.500
4dxaGSPRas-related protein Rap-1b/0.498
2cl6CAGGTPase HRas/0.497
2bmeGNPRas-related protein Rab-4A/0.495
3mjhGTPRas-related protein Rab-5A/0.492
3tklGTPRas-related protein Rab-1A/0.488
1g16GDPRas-related protein SEC4/0.487
2clsGTPRho-related GTP-binding protein Rho6/0.484
4edz0O5Hematopoietic prostaglandin D synthase/0.482
4xoiGTPTransforming protein RhoA/0.481
2xkfBX1Serine/threonine-protein kinase Nek22.7.11.10.480
4cymGCPRas-related protein Rab-32/0.480
3cphGDPRas-related protein SEC4/0.477
4cidANPEH domain-containing protein 2/0.477
4fgcPQ0NADPH-dependent 7-cyano-7-deazaguanine reductase1.7.1.130.475
4o2rGDPGTP-binding protein Rheb/0.474
3c14FOKAdenylate cyclase type 2/0.473
3c14FOKAdenylate cyclase type 5/0.473
3eg5GNPCell division control protein 42 homolog/0.473
2ic5GNPRas-related C3 botulinum toxin substrate 3/0.469
2mseGNPMHC class I alpha chain/0.466
4n3l2FNProthrombin3.4.21.50.466
3ddw055Glycogen phosphorylase, liver form2.4.1.10.465
1tu3GNPRas-related protein Rab-5A/0.464
2a9y26AAdenosine kinase2.7.1.200.463
1kt8ILPBranched-chain-amino-acid aminotransferase, mitochondrial2.6.1.420.459
2r6jNDPEugenol synthase 11.1.1.3180.459
4pkwGM6Lethal factor3.4.24.830.457
3a783EVVitamin D3 receptor/0.456
5c46GSPRas-related protein Rab-11A/0.456
3exhTPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial1.2.4.10.455
3exhTPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial1.2.4.10.455
3umsGDPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.455
4nbb9CATerminal oxygenase component of carbazole/0.455
1rzuADPGlycogen synthase 12.4.1.210.454
4oe4NADDelta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial1.2.1.880.454
1culFOKAdenylate cyclase type 2/0.453
1culFOKAdenylate cyclase type 5/0.453
2pbwDOQGlutamate receptor ionotropic, kainate 1/0.453
3iogSDFMetallo-beta-lactamase type 2/0.453
2p1v5TNRetinoic acid receptor RXR-alpha/0.452
3nmpPYVAbscisic acid receptor PYL2/0.452
4paoGSPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.452
5hpyGDPTransforming protein RhoA/0.452
1mlzPLPAdenosylmethionine-8-amino-7-oxononanoate aminotransferase2.6.1.620.451
2fhjMFNFormylmethanofuran--tetrahydromethanopterin formyltransferase2.3.1.1010.451
2hptBESAminopeptidase N3.4.11.20.451
2zznSAMtRNA (guanine(37)-N1)-methyltransferase Trm5b2.1.1.2280.451
5iqgGDPBifunctional AAC/APH2.3.10.451
1ve3SAMUncharacterized protein/0.450
1ygjRMCPyridoxal kinase2.7.1.350.450
4uj5GNPRas-related protein Rab-11A/0.450
3fhxPXLPyridoxal kinase2.7.1.350.449
2h15B19Carbonic anhydrase 24.2.1.10.448
4iteTEYVitamin D3 receptor/0.448
2bfmTOPPteridine reductase 11.5.1.330.447
2r2nKYNKynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.447
2rdn1PL1-deoxypentalenic acid 11-beta-hydroxylase1.14.11.350.447
3nh8DC2N-acyl-aromatic-L-amino acid amidohydrolase (carboxylate-forming)3.5.1.1140.447
4bamMM9Prothrombin3.4.21.50.447
4bfrJ82Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit beta isoform2.7.1.1530.447
4g0k0VSGlutathionyl-hydroquinone reductase YqjG1.80.447
3gyaCOAGCN5-related N-acetyltransferase/0.446
3t1tGDPProbable gliding protein mglA/0.446
3vhxGTPADP-ribosylation factor 6/0.446
3c16FOKAdenylate cyclase type 2/0.445
3c16FOKAdenylate cyclase type 5/0.445
3otwCOAPhosphopantetheine adenylyltransferase/0.445
3x04GNPPhosphatidylinositol 5-phosphate 4-kinase type-2 beta2.7.1.1490.445
4pnmNU1Tankyrase-22.4.2.300.445
2ic5GDPRas-related C3 botulinum toxin substrate 3/0.444
4gusFADLysine-specific histone demethylase 1B10.444
4kp61S1cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.444
4nhyPD2Prolyl 3-hydroxylase OGFOD11.14.110.444
1crbRTLRetinol-binding protein 1/0.443
1oc1ASVIsopenicillin N synthase1.21.3.10.443
1xm1GAHProthrombin3.4.21.50.443
2xk85R1Serine/threonine-protein kinase Nek22.7.11.10.443
2zsiGA4Gibberellin receptor GID1A30.443
3djfBC3Purine nucleoside phosphorylase/0.443
3dr1C5DVitamin D3 receptor A/0.443
3ozc4CTS-methyl-5'-thioadenosine phosphorylase/0.443
4aoaIK2Beta-phenylalanine transaminase2.6.10.443
5iubCLRAdenosine receptor A2a/0.443
5kf2COAPredicted acetyltransferase/0.443
1n5tOALActVA 6 protein/0.442
2qw8NAPEugenol synthase 11.1.1.3180.442
2xnpWCXSerine/threonine-protein kinase Nek22.7.11.10.442
4g2i0VQVitamin D3 receptor/0.442
5bt42LOBromodomain-containing protein 4/0.442
1aj22PHDihydropteroate synthase/0.441
1ay0TPPTransketolase 12.2.1.10.441
1gilGSPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.441
1kceCB3Thymidylate synthase/0.441
2vcwZZAHematopoietic prostaglandin D synthase/0.441
3qgd26SGenome polyprotein2.7.7.480.441
4q0a4OAVitamin D3 receptor A/0.441
5k2bZMAAdenosine receptor A2a/0.441
1cjvFOKAdenylate cyclase type 2/0.440
1cjvFOKAdenylate cyclase type 5/0.440
4uhrNGIAdenosine receptor A2a/0.440