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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
3rslGNPGTPase HRas

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity
Align
3rslGNPGTPase HRas/1.000
2rgbGNPGTPase HRas/0.778
4dlwGNPGTPase HRas/0.773
4dlzGNPGTPase HRas/0.768
2rgcGNPGTPase HRas/0.749
3rs7GNPGTPase HRas/0.735
3rs0GNPGTPase HRas/0.734
4dlvGNPGTPase HRas/0.732
4dlxGNPGTPase HRas/0.730
4dltGNPGTPase HRas/0.706
3lbnGNPGTPase HRas/0.698
3v4fGNPGTPase HRas/0.691
4g0nGNPGTPase HRas/0.689
3rs5GNPGTPase HRas/0.669
3l8yGNPGTPase HRas/0.667
3ddcGNPGTPase HRas/0.659
2rgeGNPGTPase HRas/0.657
3lbhGNPGTPase HRas/0.657
3rs4GNPGTPase HRas/0.651
5b2zGNPGTPase HRas/0.648
4dlsGNPGTPase HRas/0.647
3i3sGNPGTPase HRas/0.645
4k81GTPGTPase HRas/0.643
3kkoGNPRas-related protein M-Ras/0.642
2c5lGTPGTPase HRas/0.639
3oivGNPGTPase HRas/0.635
4l9wGNPGTPase HRas/0.635
4lhwGNPRas-related protein Rab-8A/0.635
5difGNPGTP-binding nuclear protein Ran/0.634
3oiwGNPGTPase HRas/0.632
3k8yGNPGTPase HRas/0.631
3oiuGNPGTPase HRas/0.631
3pitGNPRas-related protein M-Ras/0.625
4rkfGNPRas-related protein Rab-3/0.624
3x1zGNPRas-related protein Rap-1b/0.619
3kudGDPGTPase HRas/0.617
5dhaGNPGTP-binding nuclear protein Ran/0.614
3ea5GDPGTP-binding nuclear protein Ran/0.613
3lbiGNPGTPase HRas/0.613
4nyiGNPGTPase HRas/0.613
4dsnGCPGTPase KRas/0.607
3rabGNPRas-related protein Rab-3A/0.606
4hdoGNPRas-related protein Rap-1b/0.606
1e96GTPRas-related C3 botulinum toxin substrate 1/0.605
3kucGDPRas-related protein Rap-1A/0.605
4l9sGDPGTPase HRas/0.603
3oesGNPGTPase RhebL1/0.600
1ibrGNPGTP-binding nuclear protein Ran/0.599
3a6pGTPGTP-binding nuclear protein Ran/0.591
4nyjGNPGTPase HRas/0.590
1t91GTPRas-related protein Rab-7a/0.589
4qxaGTPRas-related protein Rab-9A/0.586
1yzqGNPRas-related protein Rab-6A/0.585
2zetGTPRas-related protein Rab-27B/0.580
3w3zGTPGTP-binding nuclear protein Ran/0.579
1xtsGTPGTP-binding protein Rheb/0.577
2bkuGTPGTP-binding nuclear protein Ran/0.577
4mitGTPRho-related protein racC/0.577
3e5hGNPRas-related protein Rab-28/0.576
1g17GNPRas-related protein SEC4/0.575
2qmeGCPRas-related C3 botulinum toxin substrate 3/0.575
4ol0GTPGTP-binding nuclear protein Ran/0.571
5jljGNPGTP-binding nuclear protein Ran/0.570
3nbzGTPGTP-binding nuclear protein Ran/0.567
1zd9GDPADP-ribosylation factor-like protein 8A/0.565
2fe4GDPRas-related protein Rab-6B/0.562
2x19GTPGTP-binding nuclear protein GSP1/CNR1/0.562
3bc1GNPRas-related protein Rab-27A/0.562
3bbpGTPRas-related protein Rab-6A/0.561
3sbeGNPRas-related C3 botulinum toxin substrate 1/0.559
2gilGTPRas-related protein Rab-6A/0.557
3wyfGTPGTP-binding nuclear protein/0.556
4hdqGNPRas-related protein Rap-1b/0.556
3sbdGNPRas-related C3 botulinum toxin substrate 1/0.555
4ql3GDPGTPase KRas/0.554
1zbdGTPRas-related protein Rab-3A/0.552
4dsoGSPGTPase KRas/0.545
2msdGNPMHC class I alpha chain/0.544
4o2lGTPGTP-binding protein Rheb/0.544
1vg8GNPRas-related protein Rab-7a/0.542
3tsoGNPRas-related protein Rab-25/0.542
3a58GNPGTP-binding protein RHO1/0.541
1xtrGNPGTP-binding protein Rheb/0.540
3th5GNPRas-related C3 botulinum toxin substrate 1/0.540
1yhnGTPRas-related protein Rab-7a/0.539
2w2xGSPRas-related C3 botulinum toxin substrate 2/0.538
4obeGDPGTPase KRas/0.538
3wygGTPGTP-binding nuclear protein GSP1/CNR1/0.536
4epxGDPGTPase KRas/0.536
4q03GDPGTPase KRas/0.536
1k5dGNPGTP-binding nuclear protein Ran/0.533
1s1cGNPTransforming protein RhoA/0.533
4epwGDPGTPase KRas/0.533
1zc4GNPRas-related protein Ral-A/0.531
2ffqGSPRas-related protein Rab-6B/0.531
4o2rGDPGTP-binding protein Rheb/0.530
1zc3GNPRas-related protein Ral-A/0.528
4tq9GDPGTPase KRas/0.528
1kmqGNPTransforming protein RhoA/0.527
4ldjGDPGTPase KRas/0.527
4kvgGTPRas-related protein Rap-1A/0.526
1a2bGSPTransforming protein RhoA/0.525
3tnfGNPRas-related protein Rab-8A/0.525
3lawGNPRas-related protein Rab-7a/0.524
3tgpGNPGTPase HRas/0.522
4lucGDPGTPase KRas/0.522
4wa7GDPGTPase KRas/0.519
4lv6GDPGTPase KRas/0.518
3kz1GSPTransforming protein RhoA/0.517
1oixGDPRas-related protein Rab-11A/0.516
2ce2GDPGTPase HRas/0.515
4uj3GNPRas-related protein Rab-11A/0.515
1m7bGTPRho-related GTP-binding protein RhoE/0.513
3kkqGDPRas-related protein M-Ras/0.512
3mjhGTPRas-related protein Rab-5A/0.512
4q02GDPGTPase KRas/0.511
2ov2GCPRas-related C3 botulinum toxin substrate 3/0.510
1cxzGSPTransforming protein RhoA/0.509
4lpkGDPGTPase KRas/0.509
4ead0NPThymidine phosphorylase2.4.2.40.508
1mh1GNPRas-related C3 botulinum toxin substrate 1/0.507
2gcpGSPRho-related GTP-binding protein RhoC/0.507
4xvrGNPGTPase HRas/0.505
1x1rGDPRas-related protein M-Ras/0.501
2clsGTPRho-related GTP-binding protein Rho6/0.501
2p2lGDPRas-related C3 botulinum toxin substrate 1/0.501
4l8gGDPGTPase KRas/0.501
4o25GTPGTP-binding protein Rheb/0.501
1ow3GDPTransforming protein RhoA/0.497
2fjuGSPRas-related C3 botulinum toxin substrate 1/0.497
4dxaGSPRas-related protein Rap-1b/0.495
4xvqGNPGTPase HRas/0.495
3cphGDPRas-related protein SEC4/0.494
1lfdGNPGTPase HRas/0.493
1d5cGDPGTPase (Rab6)/0.490
4gzlGNPRas-related C3 botulinum toxin substrate 1/0.490
2rdn1PL1-deoxypentalenic acid 11-beta-hydroxylase1.14.11.350.489
2rggGNPGTPase HRas/0.489
3eg5GNPCell division control protein 42 homolog/0.489
3sfxJANUncharacterized protein/0.487
2bmeGNPRas-related protein Rab-4A/0.486
1z2aGDPRas-related protein Rab-23/0.481
4xoiGTPTransforming protein RhoA/0.481
1yu9GNPRas-related protein Rab-4A/0.480
2gvdFKPAdenylate cyclase type 2/0.479
2gvdFKPAdenylate cyclase type 5/0.479
3gmd2M3Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.479
4cymGCPRas-related protein Rab-32/0.479
2mscGDPMHC class I alpha chain/0.478
3c14FOKAdenylate cyclase type 2/0.477
3c14FOKAdenylate cyclase type 5/0.477
1ay0TPPTransketolase 12.2.1.10.476
4lrwGDPGTPase KRas/0.476
3vt45YIVitamin D3 receptor/0.473
1mrqSTRAldo-keto reductase family 1 member C1/0.472
2a1hGBNBranched-chain-amino-acid aminotransferase, mitochondrial2.6.1.420.472
2j5xGSPADP-ribosylation factor 6/0.472
4js0GNPCell division control protein 42 homolog/0.471
1tu3GNPRas-related protein Rab-5A/0.470
2hamC33Vitamin D3 receptor/0.470
1z0dGDPRas-related protein Rab-5C/0.469
4cidANPEH domain-containing protein 2/0.469
5hpyGDPTransforming protein RhoA/0.469
5kf1COAPredicted acetyltransferase/0.467
1uadGNPRas-related protein Ral-A/0.466
2fg5GNPRas-related protein Rab-31/0.466
2xpvMIYTetracycline repressor protein class D/0.466
3t1tGDPProbable gliding protein mglA/0.466
3qbtGNPRas-related protein Rab-8A/0.464
1n5tOALActVA 6 protein/0.462
2eklNADD-3-phosphoglycerate dehydrogenase/0.462
3x1wGDPRas-related protein Rap-1b/0.462
4dsuGDPGTPase KRas/0.462
4kp61S1cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.462
5li5THR_ALA_ASN_PRO_SEPKLTH0G14146p/0.462
2xtzGSPGuanine nucleotide-binding protein alpha-1 subunit/0.461
4o9cCOAAcetyl-CoA acetyltransferase2.3.1.90.461
5iu4ZMAAdenosine receptor A2a/0.461
2mseGNPMHC class I alpha chain/0.460
1d0lBLGMembrane-bound lytic murein transglycosylase B4.2.2.n10.459
1g16GDPRas-related protein SEC4/0.459
2xkfBX1Serine/threonine-protein kinase Nek22.7.11.10.459
4uj5GNPRas-related protein Rab-11A/0.459
1z2cGNPRho-related GTP-binding protein RhoC/0.458
3gyaCOAGCN5-related N-acetyltransferase/0.458
3pqbVGPPutative oxidoreductase/0.458
1cjtFOKAdenylate cyclase type 2/0.457
1cjtFOKAdenylate cyclase type 5/0.457
1lcbDHFThymidylate synthase/0.457
1p8dCO1Oxysterols receptor LXR-beta/0.457
2g0nGDPRas-related C3 botulinum toxin substrate 3/0.457
3tklGTPRas-related protein Rab-1A/0.457
1gwnGTPRho-related GTP-binding protein RhoE/0.456
2ic5GNPRas-related C3 botulinum toxin substrate 3/0.456
2v5aLZLBiotin carboxylase6.3.4.140.456
2vbpVB1Isopenicillin N synthase1.21.3.10.456
3k7mFAD6-hydroxy-L-nicotine oxidase/0.456
1ro98BRcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.455
2fhkMFNFormylmethanofuran--tetrahydromethanopterin formyltransferase2.3.1.1010.455
4rraA3TProbable threonine--tRNA ligase 26.1.1.30.455
1rkhVD2Vitamin D3 receptor/0.454
1xomCIOcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.454
3c15FOKAdenylate cyclase type 2/0.454
3c15FOKAdenylate cyclase type 5/0.454
3exhTPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial1.2.4.10.454
3exhTPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial1.2.4.10.454
3ha5SFGHydroxymycolate synthase MmaA42.1.10.454
3up0D7SaceDAF-12/0.454
3w0aDS5Vitamin D3 receptor/0.454
4la7A1OAbscisic acid receptor PYL2/0.454
4lb2DM5Serum albumin/0.454
1jtvTESEstradiol 17-beta-dehydrogenase 11.1.1.620.453
1xu9CPSCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.453
2cy0NAPShikimate dehydrogenase (NADP(+))/0.453
3w0c6DSVitamin D3 receptor/0.453
4rr7A3SProbable threonine--tRNA ligase 26.1.1.30.453
3sqxANPATP-dependent RNA helicase MSS116, mitochondrial3.6.4.130.452
3zeiAWHO-acetylserine sulfhydrylase/0.452
2z9dFMNFMN-dependent NADH-azoreductase/0.451
2zruFMNIsopentenyl-diphosphate delta-isomerase/0.451
3em0CHDFatty acid-binding protein 6, ileal (gastrotropin)/0.451
4q0a4OAVitamin D3 receptor A/0.451
3i5xANPATP-dependent RNA helicase MSS116, mitochondrial3.6.4.130.450
3tbaADPRibonucleoside-diphosphate reductase large chain 11.17.4.10.450
4bfwZVWPantothenate kinase2.7.1.330.450
4zu44TGWxcM-like protein/0.450
1oxoIK2Aspartate aminotransferase, mitochondrial2.6.1.10.449
2zlcVDXVitamin D3 receptor/0.449
3p8iFMNPentaerythritol tetranitrate reductase/0.449
3stv3HOMethylketone synthase I/0.449
4panGDPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.449
5c46GSPRas-related protein Rab-11A/0.449
1cjuFOKAdenylate cyclase type 2/0.448
1cjuFOKAdenylate cyclase type 5/0.448
1x1cSAHC-20 methyltransferase/0.448
2abjCBCBranched-chain-amino-acid aminotransferase, cytosolic2.6.1.420.448
2b36NADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.448
2cl6CAGGTPase HRas/0.448
3a783EVVitamin D3 receptor/0.448
4qzuRTLRetinol-binding protein 2/0.448
2hb7O1CVitamin D3 receptor/0.447
2xpwOTCTetracycline repressor protein class D/0.447
3bj7COADiamine acetyltransferase 1/0.447
3gy9COAGCN5-related N-acetyltransferase/0.447
4xba5GPAprataxin-like protein30.447
2r2lPB9Protein farnesyltransferase subunit beta2.5.1.580.446
2xvfFADPutative flavin-containing monooxygenase/0.446
4ixd1HVIntegrin alpha-L/0.446
4rr6A3SProbable threonine--tRNA ligase 26.1.1.30.446
1k02FMNNADPH dehydrogenase 11.6.99.10.445
1qyw5SDEstradiol 17-beta-dehydrogenase 11.1.1.620.445
2hb8MVDVitamin D3 receptor/0.445
2oegUPGUDP-glucose pyrophosphorylase/0.445
3sqwANPATP-dependent RNA helicase MSS116, mitochondrial3.6.4.130.445
3zbnCOA3-ketoacyl-CoA thiolase-like protein/0.445
4iteTEYVitamin D3 receptor/0.445
1icsFMN12-oxophytodienoate reductase 11.3.1.420.444
2b4qNAPRhamnolipids biosynthesis 3-oxoacyl-[acyl-carrier-protein] reductase1.1.1.1000.444
2p9cNAID-3-phosphoglycerate dehydrogenase1.1.1.950.444
1bwlFMNNADPH dehydrogenase 11.6.99.10.443
1upw444Oxysterols receptor LXR-beta/0.443
1z0aGDPRas-related protein Rab-2A/0.443
1zgaHMKIsoflavone 4'-O-methyltransferase/0.443
2e0nSAHPrecorrin-2 C20-methyltransferase/0.443
2xk4OL2Serine/threonine-protein kinase Nek22.7.11.10.443
3ddw055Glycogen phosphorylase, liver form2.4.1.10.443
3kozZ97D-ornithine 4,5-aminomutase subunit beta/0.443
4b2gV1NUncharacterized protein/0.443
4g2l0WLHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.443
4wbnGTPTubulin alpha-1B chain/0.443
1hb3SCVIsopenicillin N synthase1.21.3.10.442
2jb4A14Isopenicillin N synthase1.21.3.10.442
3ghvGHCDihydrofolate reductase1.5.1.30.442
3kslSZHProtein farnesyltransferase subunit beta2.5.1.580.442
4h9tHL4Phosphotriesterase/0.442
4jicFMNGTN Reductase/0.442
1kt8ILPBranched-chain-amino-acid aminotransferase, mitochondrial2.6.1.420.441
1lcbTMPThymidylate synthase/0.441
1u0hFOKAdenylate cyclase type 2/0.441
1u0hFOKAdenylate cyclase type 5/0.441
2e98B29Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.441
2fm0M98cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.441
2trtTACTetracycline repressor protein class D/0.441
2vczVC3Hematopoietic prostaglandin D synthase/0.441
3umsGDPGuanine nucleotide-binding protein G(i) subunit alpha-1/0.441
4g20484Vitamin D3 receptor A/0.441
4n3l2FNProthrombin3.4.21.50.441
3emlZMAAdenosine receptor A2a/0.441
1bcpATPPertussis toxin subunit 4/0.440
1bcpATPPertussis toxin subunit 5/0.440
1n4pCYS_VAL_ILE_LEU_GERGeranylgeranyl transferase type-1 subunit beta2.5.1.590.440
1obnASVIsopenicillin N synthase1.21.3.10.440
2nsd4PIEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.440
2o4jVD4Vitamin D3 receptor/0.440
3c15GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.440
3lxeTORCarbonic anhydrase 14.2.1.10.440
3nmpPYVAbscisic acid receptor PYL2/0.440
3q7fED2Uncharacterized protein/0.440
3vv8B02Beta-secretase 13.4.23.460.440
4boeCLRJapanin/0.440
4gz612VUDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit/0.440
4k2xFADPolyketide oxygenase/hydroxylase/0.440
5jtbZMAAdenosine receptor A2a/0.440