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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
4hdoGNPRas-related protein Rap-1b

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
4hdoGNPRas-related protein Rap-1b/1.000
3lbiGNPGTPase HRas/0.668
2c5lGTPGTPase HRas/0.659
3v4fGNPGTPase HRas/0.657
3pitGNPRas-related protein M-Ras/0.652
3l8yGNPGTPase HRas/0.648
4dsnGCPGTPase KRas/0.647
3oiwGNPGTPase HRas/0.646
4g0nGNPGTPase HRas/0.645
5b2zGNPGTPase HRas/0.642
3lbnGNPGTPase HRas/0.640
2rgbGNPGTPase HRas/0.639
2gilGTPRas-related protein Rab-6A/0.635
3a6pGTPGTP-binding nuclear protein Ran/0.633
3lbhGNPGTPase HRas/0.628
4dltGNPGTPase HRas/0.627
2rgcGNPGTPase HRas/0.626
4mitGTPRho-related protein racC/0.625
3x1zGNPRas-related protein Rap-1b/0.623
4k81GTPGTPase HRas/0.623
1t91GTPRas-related protein Rab-7a/0.621
3bbpGTPRas-related protein Rab-6A/0.620
2qmeGCPRas-related C3 botulinum toxin substrate 3/0.619
3e5hGNPRas-related protein Rab-28/0.619
3oivGNPGTPase HRas/0.619
3rs4GNPGTPase HRas/0.617
3ddcGNPGTPase HRas/0.616
3oiuGNPGTPase HRas/0.616
3rabGNPRas-related protein Rab-3A/0.616
3sbdGNPRas-related C3 botulinum toxin substrate 1/0.615
1ibrGNPGTP-binding nuclear protein Ran/0.614
2rgeGNPGTPase HRas/0.612
4nyjGNPGTPase HRas/0.610
5dhaGNPGTP-binding nuclear protein Ran/0.609
3w3zGTPGTP-binding nuclear protein Ran/0.608
4dlzGNPGTPase HRas/0.607
3i3sGNPGTPase HRas/0.606
1xtsGTPGTP-binding protein Rheb/0.605
1yzqGNPRas-related protein Rab-6A/0.605
3rslGNPGTPase HRas/0.605
3rs7GNPGTPase HRas/0.603
3kkoGNPRas-related protein M-Ras/0.601
3a58GNPGTP-binding protein RHO1/0.599
3k8yGNPGTPase HRas/0.598
4rkfGNPRas-related protein Rab-3/0.595
5difGNPGTP-binding nuclear protein Ran/0.595
4lhwGNPRas-related protein Rab-8A/0.594
4nyiGNPGTPase HRas/0.594
4dlxGNPGTPase HRas/0.593
3kudGDPGTPase HRas/0.590
3rs5GNPGTPase HRas/0.589
4dlwGNPGTPase HRas/0.589
4o25GTPGTP-binding protein Rheb/0.587
1xtrGNPGTP-binding protein Rheb/0.586
3oesGNPGTPase RhebL1/0.586
3wyfGTPGTP-binding nuclear protein/0.586
4dlsGNPGTPase HRas/0.584
1a2bGSPTransforming protein RhoA/0.583
1e96GTPRas-related C3 botulinum toxin substrate 1/0.583
2gcpGSPRho-related GTP-binding protein RhoC/0.580
3kucGDPRas-related protein Rap-1A/0.580
1yhnGTPRas-related protein Rab-7a/0.579
4l9wGNPGTPase HRas/0.578
1zc3GNPRas-related protein Ral-A/0.576
1zbdGTPRas-related protein Rab-3A/0.575
3sbeGNPRas-related C3 botulinum toxin substrate 1/0.575
3rs0GNPGTPase HRas/0.573
1zd9GDPADP-ribosylation factor-like protein 8A/0.569
3ea5GDPGTP-binding nuclear protein Ran/0.569
4o2lGTPGTP-binding protein Rheb/0.569
4ol0GTPGTP-binding nuclear protein Ran/0.569
1g17GNPRas-related protein SEC4/0.567
4dlvGNPGTPase HRas/0.567
1kmqGNPTransforming protein RhoA/0.566
4kvgGTPRas-related protein Rap-1A/0.566
1s1cGNPTransforming protein RhoA/0.565
3tgpGNPGTPase HRas/0.565
2w2xGSPRas-related C3 botulinum toxin substrate 2/0.563
4dsoGSPGTPase KRas/0.563
2fe4GDPRas-related protein Rab-6B/0.562
4qxaGTPRas-related protein Rab-9A/0.562
2bkuGTPGTP-binding nuclear protein Ran/0.560
1cxzGSPTransforming protein RhoA/0.555
1zc4GNPRas-related protein Ral-A/0.554
3nbzGTPGTP-binding nuclear protein Ran/0.554
2msdGNPMHC class I alpha chain/0.551
1vg8GNPRas-related protein Rab-7a/0.550
3eg5GNPCell division control protein 42 homolog/0.550
5jljGNPGTP-binding nuclear protein Ran/0.550
3tsoGNPRas-related protein Rab-25/0.549
1yu9GNPRas-related protein Rab-4A/0.548
2zetGTPRas-related protein Rab-27B/0.548
4hdqGNPRas-related protein Rap-1b/0.546
4js0GNPCell division control protein 42 homolog/0.543
1m7bGTPRho-related GTP-binding protein RhoE/0.542
2ov2GCPRas-related C3 botulinum toxin substrate 3/0.541
2fjuGSPRas-related C3 botulinum toxin substrate 1/0.540
4tq9GDPGTPase KRas/0.539
2x19GTPGTP-binding nuclear protein GSP1/CNR1/0.538
3mjhGTPRas-related protein Rab-5A/0.538
4l9sGDPGTPase HRas/0.538
4lpkGDPGTPase KRas/0.537
1n6lGTPRas-related protein Rab-5A/0.536
3tklGTPRas-related protein Rab-1A/0.535
3th5GNPRas-related C3 botulinum toxin substrate 1/0.534
3lawGNPRas-related protein Rab-7a/0.532
4uj3GNPRas-related protein Rab-11A/0.531
3tnfGNPRas-related protein Rab-8A/0.530
3qbtGNPRas-related protein Rab-8A/0.529
1d5cGDPGTPase (Rab6)/0.527
1k5dGNPGTP-binding nuclear protein Ran/0.527
2ffqGSPRas-related protein Rab-6B/0.525
2rggGNPGTPase HRas/0.525
4lucGDPGTPase KRas/0.525
4obeGDPGTPase KRas/0.524
2fg5GNPRas-related protein Rab-31/0.523
2ce2GDPGTPase HRas/0.520
4o2rGDPGTP-binding protein Rheb/0.517
1g16GDPRas-related protein SEC4/0.514
4ql3GDPGTPase KRas/0.513
4xvrGNPGTPase HRas/0.511
3cphGDPRas-related protein SEC4/0.510
3wygGTPGTP-binding nuclear protein GSP1/CNR1/0.510
3kz1GSPTransforming protein RhoA/0.507
3k9lGNPGTPase HRas/0.506
4d0lGSPRas-related protein Rab-11A/0.506
1mh1GNPRas-related C3 botulinum toxin substrate 1/0.505
3kkqGDPRas-related protein M-Ras/0.505
4uj5GNPRas-related protein Rab-11A/0.505
4xoiGTPTransforming protein RhoA/0.505
2j5xGSPADP-ribosylation factor 6/0.504
4cymGCPRas-related protein Rab-32/0.504
4epxGDPGTPase KRas/0.504
4dxaGSPRas-related protein Rap-1b/0.503
5hpyGDPTransforming protein RhoA/0.503
1oixGDPRas-related protein Rab-11A/0.501
5c46GSPRas-related protein Rab-11A/0.501
4q03GDPGTPase KRas/0.500
1lfdGNPGTPase HRas/0.497
2mseGNPMHC class I alpha chain/0.496
3bc1GNPRas-related protein Rab-27A/0.494
4lv6GDPGTPase KRas/0.493
2clsGTPRho-related GTP-binding protein Rho6/0.492
1gwnGTPRho-related GTP-binding protein RhoE/0.490
1tu3GNPRas-related protein Rab-5A/0.489
4gzlGNPRas-related C3 botulinum toxin substrate 1/0.489
2gvdGSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.488
4lrwGDPGTPase KRas/0.486
4gzmGSPRas-related C3 botulinum toxin substrate 1/0.485
4q02GDPGTPase KRas/0.485
4xvqGNPGTPase HRas/0.485
1jtvTESEstradiol 17-beta-dehydrogenase 11.1.1.620.484
3umsGDPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.484
4l8gGDPGTPase KRas/0.484
1z2aGDPRas-related protein Rab-23/0.483
4wa7GDPGTPase KRas/0.483
3t1tGDPProbable gliding protein mglA/0.482
1culGSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.481
1z0aGDPRas-related protein Rab-2A/0.481
1z2cGNPRho-related GTP-binding protein RhoC/0.481
2p2lGDPRas-related C3 botulinum toxin substrate 1/0.481
3gmd2M3Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.478
4ldjGDPGTPase KRas/0.478
3c14GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.477
3x1wGDPRas-related protein Rap-1b/0.476
4dsuGDPGTPase KRas/0.476
4gojGNPADP-ribosylation factor-like protein 3/0.475
1ky2GNPGTP-binding protein YPT7/0.474
1y3aGDPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.473
4epwGDPGTPase KRas/0.473
1ow3GDPTransforming protein RhoA/0.471
2g0nGDPRas-related C3 botulinum toxin substrate 3/0.470
3dheANDEstradiol 17-beta-dehydrogenase 11.1.1.620.470
3r9xGNPGTPase Era/0.469
5di3GNPADP-ribosylation factor-like protein 3/0.466
1q0zAKAAclacinomycin methylesterase RdmC3.1.1.950.465
3cx6GDPGuanine nucleotide-binding protein subunit alpha-13/0.465
1m4iCOAAminoglycoside 2'-N-acetyltransferase2.3.10.464
1x1dSAHC-20 methyltransferase/0.463
2gvdFKPAdenylate cyclase type 2/0.463
2gvdFKPAdenylate cyclase type 5/0.463
2ohjFMNType A flavoprotein FprA10.463
1giaGSPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.461
3r7wGNPGTP-binding protein GTR2/0.461
4dbzNDPPutative ketoacyl reductase1.3.10.461
2xtzGSPGuanine nucleotide-binding protein alpha-1 subunit/0.459
3w0c6DSVitamin D3 receptor/0.459
1rzuADPGlycogen synthase 12.4.1.210.458
2bmeGNPRas-related protein Rab-4A/0.458
2xvfFADPutative flavin-containing monooxygenase/0.458
3maaFKPAdenylate cyclase type 2/0.457
3maaFKPAdenylate cyclase type 5/0.457
3pqbVGPPutative oxidoreductase/0.457
1tehNADAlcohol dehydrogenase class-31.1.1.10.456
3ozc4CTS-methyl-5'-thioadenosine phosphorylase/0.456
1x1rGDPRas-related protein M-Ras/0.455
1ia4TQ6Dihydrofolate reductase1.5.1.30.454
1w7h3IPMitogen-activated protein kinase 14/0.453
2mscGDPMHC class I alpha chain/0.453
2xrlDXTTetracycline repressor protein class D/0.453
4dvgGSPRho family GTPase/0.453
1m78NDPDihydrofolate reductase1.5.1.30.452
1p91SAM23S rRNA (guanine(745)-N(1))-methyltransferase/0.452
1rx1NAPDihydrofolate reductase1.5.1.30.452
4buv16ITankyrase-22.4.2.300.451
4uy6SAHHistidine N-alpha-methyltransferase/0.451
1dj3GDPAdenylosuccinate synthetase, chloroplastic/0.450
4b3aTACTetracycline repressor protein class D/0.450
3h3sH15Collagen type IV alpha-3-binding protein/0.449
4kp61S1cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.449
4plpNADHomospermidine synthase2.5.1.440.448
1ay0TPPTransketolase 12.2.1.10.447
1cq7PY5Aspartate aminotransferase2.6.1.10.447
1cs4GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.447
1iolESTEstradiol 17-beta-dehydrogenase 11.1.1.620.447
1x1aSAMC-20 methyltransferase/0.447
1x1bSAHC-20 methyltransferase/0.447
1xs7MMIBeta-secretase 13.4.23.460.447
3dh8B4NUncharacterized protein PA1000/0.447
3f63GTXGlutathione transferase GST1-4/0.447
4q71FADBifunctional protein PutA/0.447
1orkATCTetracycline repressor protein class D/0.446
3vf60H6Glucokinase2.7.1.20.446
3w0aDS5Vitamin D3 receptor/0.446
3w0yDS4Vitamin D3 receptor/0.446
4l0qNADAlcohol dehydrogenase class-3/0.446
1tkbN1TTransketolase 12.2.1.10.445
2xpuTDCTetracycline repressor protein class D/0.445
4bfxZVXPantothenate kinase2.7.1.330.445
4g2i0VQVitamin D3 receptor/0.445
4j8tDOGUncharacterized PhzA/B-like protein PA3332/0.445
4v2gITCTetracycline repressor protein class D/0.445
1yreCOAUncharacterized protein/0.444
2fhjMFNFormylmethanofuran--tetrahydromethanopterin formyltransferase2.3.1.1010.444
2q3fGNPRas-related GTP-binding protein D/0.444
2rdn1PL1-deoxypentalenic acid 11-beta-hydroxylase1.14.11.350.444
2ydvNECAdenosine receptor A2a/0.444
3c15GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.444
3tfuPL8Adenosylmethionine-8-amino-7-oxononanoate aminotransferase2.6.1.620.444
1q12ATPMaltose/maltodextrin import ATP-binding protein MalK/0.443
2i65NADADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 13.2.2.60.443
3i0pNADMalate dehydrogenase, putative/0.443
3naxMP73-phosphoinositide-dependent protein kinase 12.7.11.10.443
3qe0GDPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.443
4auxXTCTetracycline repressor protein class D/0.443
4cidANPEH domain-containing protein 2/0.443
1q0rAKTAclacinomycin methylesterase RdmC3.1.1.950.442
1vrwNAIEnoyl-ACP reductase/0.442
2vkeTACTetracycline repressor protein class D/0.442
3dgaNDPBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.441
3gdpFAD(R)-mandelonitrile lyase 24.1.2.100.441
3qpg3QPAspartate aminotransferase2.6.1.10.441
4ead0NPThymidine phosphorylase2.4.2.40.441
1gilGSPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.440
1gotGDPGuanine nucleotide-binding protein G(t) subunit alpha-1/0.440
1kt6RTLRetinol-binding protein 4/0.440
1xmmM7Gm7GpppX diphosphatase3.6.1.590.440
3djfBC3Purine nucleoside phosphorylase/0.440
3em0CHDFatty acid-binding protein 6, ileal (gastrotropin)/0.440
3mpiFADGlutaryl-CoA dehydrogenase1.3.99.320.440