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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
3fbcTYDNucleoside diphosphate kinase2.7.4.6

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
3fbcTYDNucleoside diphosphate kinase2.7.4.61.000
3fbeGDPNucleoside diphosphate kinase2.7.4.60.564
3nguADPNucleoside diphosphate kinase/0.553
2hvdADPNucleoside diphosphate kinase A2.7.4.60.532
1buxPPSNucleoside diphosphate kinase, cytosolic2.7.4.60.529
1ndcTYDNucleoside diphosphate kinase, cytosolic2.7.4.60.529
3q8uADPNucleoside diphosphate kinase/0.526
3v0o4GWHisto-blood group ABO system transferase/0.518
1wklATPNucleoside diphosphate kinase/0.515
3v0p4GWHisto-blood group ABO system transferase/0.500
1nhkCMPNucleoside diphosphate kinase2.7.4.60.499
3p3c3P3UDP-3-O-acyl-N-acetylglucosamine deacetylase/0.490
2r8pT6FTransketolase 1/0.485
3hj9FMNUncharacterized protein/0.482
5dp2NAPCurF/0.481
1zs6ADPNucleoside diphosphate kinase 32.7.4.60.480
1cbrREACellular retinoic acid-binding protein 1/0.478
1g3mPCQEstrogen sulfotransferase2.8.2.40.476
5droZH2UDP-3-O-acyl-N-acetylglucosamine deacetylase/0.476
3gwfFADCyclohexanone monooxygenase/0.475
3h5sH5SGenome polyprotein2.7.7.480.475
1xdpATPPolyphosphate kinase/0.474
3nmpPYVAbscisic acid receptor PYL2/0.473
3wqmB29Diterpene synthase3.1.7.80.471
3t8vBTJM1 family aminopeptidase3.4.110.469
3zkyWT4Isopenicillin N synthase1.21.3.10.469
1nmkSFMPeptidyl-prolyl cis-trans isomerase A5.2.1.80.468
2ivpATPtRNA N6-adenosine threonylcarbamoyltransferase/0.467
2r8oT5XTransketolase 1/0.467
1z4uPH9Polyprotein/0.466
2ylxFADPhenylacetone monooxygenase1.14.13.920.466
4bb3KKAIsopenicillin N synthase1.21.3.10.466
2hveADPNucleoside diphosphate kinase A2.7.4.60.465
3ioeA7DPantothenate synthetase6.3.2.10.465
3uph0C1Genome polyprotein2.7.7.480.465
4bvaT3Ketimine reductase mu-crystallin1.5.1.250.465
2az3CDPNucleoside diphosphate kinase/0.463
3fhyATPPyridoxal kinase2.7.1.350.463
3h59H59Genome polyprotein2.7.7.480.463
3h5uH5UGenome polyprotein2.7.7.480.463
4g1nNZTPyruvate kinase PKM2.7.1.400.463
4nt3ZAWLactoperoxidase1.11.1.70.463
4qvhCOAPhosphopantetheinyl transferase PptT (CoA:APO-[ACP]pantetheinephosphotransferase) (CoA:APO-[acyl-carrier protein]pantetheinephosphotransferase)/0.463
1kquBR4Phospholipase A2, membrane associated/0.462
1zioAP5Adenylate kinase/0.461
3d5m4MSGenome polyprotein2.7.7.480.461
3dd125DGlycogen phosphorylase, liver form2.4.1.10.461
4pzsACOHistone acetyltransferase p300/0.461
1fmlRTLRetinol dehydratase/0.460
2z7hGG3Geranylgeranyl pyrophosphate synthase/0.460
3upi0C2Genome polyprotein2.7.7.480.460
4bfyZVYPantothenate kinase2.7.1.330.460
4ugaQ05Nitric oxide synthase oxygenase1.14.13.1650.460
1a8rGTPGTP cyclohydrolase 13.5.4.160.459
2ptfFMNUncharacterized protein MTH_863/0.459
1gsfEAAGlutathione S-transferase A12.5.1.180.458
2yxuATPPyridoxal kinase2.7.1.350.458
3bl7DD1m7GpppX diphosphatase3.6.1.590.458
4du82P0Mevalonate diphosphate decarboxylase/0.458
4gyzD5MTyrosyl-DNA phosphodiesterase 23.1.40.457
1n3rGTPGTP cyclohydrolase 13.5.4.160.456
1x1cSAHC-20 methyltransferase/0.456
3i5xANPATP-dependent RNA helicase MSS116, mitochondrial3.6.4.130.456
3il4ACO3-oxoacyl-[acyl-carrier-protein] synthase 3/0.456
3keuATPPyridoxal kinase2.7.1.350.456
3qiyQI1Botulinum neurotoxin type A3.4.24.690.456
3sqwANPATP-dependent RNA helicase MSS116, mitochondrial3.6.4.130.456
4q5jANPProtein BRASSINOSTEROID INSENSITIVE 12.7.10.10.456
2d1cNAPIsocitrate dehydrogenase [NADP]1.1.1.420.455
2ivnANPtRNA N6-adenosine threonylcarbamoyltransferase/0.455
3x025GPPhosphatidylinositol 5-phosphate 4-kinase type-2 beta2.7.1.1490.455
4ttaFMCPurine nucleoside phosphorylase DeoD-type/0.455
4yaw2AMNADPH--cytochrome P450 reductase/0.455
2fgjATPAlpha-hemolysin translocation ATP-binding protein HlyB/0.454
2gc8885Polyprotein/0.454
4qjqOTRLactoperoxidase/0.454
1nueGDPNucleoside diphosphate kinase B2.7.4.60.453
1z6tADPApoptotic protease-activating factor 1/0.453
3ozd4CTS-methyl-5'-thioadenosine phosphorylase/0.453
3zhuTD8Multifunctional 2-oxoglutarate metabolism enzyme1.2.4.20.453
4ih61EPGenome polyprotein2.7.7.480.453
5ej6TD62-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase/0.453
2oliIOPBasic phospholipase A2 VRV-PL-VIIIa3.1.1.40.452
3h65I2C5,10-methenyltetrahydromethanopterin hydrogenase1.12.98.20.452
3junAKDPhenazine biosynthesis protein A/B/0.452
4h1e10JBeta-secretase 13.4.23.460.452
4kc4WS3Histo-blood group ABO system transferase/0.452
4la7A1OAbscisic acid receptor PYL2/0.452
4oze24GUDP-3-O-acyl-N-acetylglucosamine deacetylase/0.452
4xnw2IDP2Y purinoceptor 1/0.452
2vssACOHydroxycinnamoyl-CoA hydratase-lyase4.1.2.410.451
2y1tDUDSPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS3.6.1.230.451
4dk70KSOxysterols receptor LXR-beta/0.451
5iqgGDPBifunctional AAC/APH2.3.10.451
1dxyNADD-2-hydroxyisocaproate dehydrogenase1.1.10.450
1ppjANYCytochrome b/0.450
3dl0AP5Adenylate kinase/0.450
1cbqRE9Cellular retinoic acid-binding protein 2/0.449
1hk1T44Serum albumin/0.449
1i5rHYCEstradiol 17-beta-dehydrogenase 11.1.1.620.449
1mdtAPUDiphtheria toxin/0.449
1nqw5YL6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.449
1xefATPAlpha-hemolysin translocation ATP-binding protein HlyB/0.449
3zoiM2WIsopenicillin N synthase1.21.3.10.449
4xnhACON-terminal acetyltransferase A complex subunit NAT52.3.10.449
5dozNDPJamJ/0.449
2dphNADFormaldehyde dismutase/0.448
2h447CAcGMP-specific 3',5'-cyclic phosphodiesterase/0.448
2yoj8Y6Genome polyprotein2.7.7.480.448
3q44D50M1 family aminopeptidase3.4.110.448
3slkNDPPolyketide synthase extender module 2/0.448
4mkhAP5Adenylate kinase/0.448
1yvfPH7Polyprotein/0.447
2nr4FMNConserved protein/0.447
3cvkN34Genome polyprotein2.7.7.480.447
3frkTQPQdtB/0.447
3w0yDS4Vitamin D3 receptor/0.447
4cpdNADAlcohol dehydrogenase/0.447
5iqiGNPBifunctional AAC/APH2.3.10.447
2r0cFADPutative FAD-monooxygenase/0.446
3ceaNADMyo-inositol 2-dehydrogenase-like (Promiscuous)/0.446
3jpuTY4Transcriptional activator protein LasR/0.446
3zv64HBCis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase1.3.1.560.446
4g2i0VQVitamin D3 receptor/0.446
4jvnYUGEstrogen sulfotransferase2.8.2.40.446
4r81FMNPredicted NADH dehydrogenase/0.446
4uy6SAHHistidine N-alpha-methyltransferase/0.446
1qoqIGPTryptophan synthase alpha chain/0.445
2vtdLKMUDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.445
2ym2FADPhenylacetone monooxygenase1.14.13.920.445
3thrC2FGlycine N-methyltransferase2.1.1.200.445
4dliIRGMitogen-activated protein kinase 14/0.445
4nieNBHNuclear receptor ROR-gamma/0.445
4qfyDCPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.445
4uofDATNucleoside diphosphate kinase/0.445
1jmfUMPThymidylate synthase/0.444
2i51FMNPyridoxamine 5'-phosphate oxidase-related, FMN-binding/0.444
2xk6EQHSerine/threonine-protein kinase Nek22.7.11.10.444
2yyyNAPGlyceraldehyde-3-phosphate dehydrogenase1.2.1.590.444
4geb0LDKynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.444
4mk728OGenome polyprotein2.7.7.480.444
4n3l2FNProthrombin3.4.21.50.444
5ebuFMNLactate oxidase/0.444
5kgpACOPredicted acetyltransferase/0.444
1ho5ADNProtein UshA3.1.3.50.443
1rq1FADEndoplasmic oxidoreductin-11.8.40.443
2pdtFADVivid PAS protein VVD/0.443
3h3t16HCollagen type IV alpha-3-binding protein/0.443
3iocA5DPantothenate synthetase6.3.2.10.443
3q7jFBOTricorn protease-interacting factor F33.4.110.443
4b2gV1NUncharacterized protein/0.443
4uohADPNucleoside diphosphate kinase/0.443
4wfr2AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.443
1hncGDNGlutathione S-transferase Mu 22.5.1.180.442
1thnADPAnti-sigma F factor/0.442
1u8vFAD4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase/0.442
1uagUMAUDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.442
2hq9FADMll6688 protein/0.442
3biy01KHistone acetyltransferase p300/0.442
3ska053Genome polyprotein2.7.7.480.442
3up4FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.442
4jvmXDIEstrogen sulfotransferase2.8.2.40.442
1al8DHPPeroxisomal (S)-2-hydroxy-acid oxidase1.1.3.150.441
1aquESTEstrogen sulfotransferase, testis isoform2.8.2.40.441
1qjfACSIsopenicillin N synthase1.21.3.10.441
1ykiFMNOxygen-insensitive NAD(P)H nitroreductase/0.441
1ysiN3BBcl-2-like protein 1/0.441
2ddoATPPyridoxine/pyridoxal/pyridoxamine kinase/0.441
3arpDEQChitinase A/0.441
3jynNDPQuinone oxidoreductase/0.441
3mqe416Prostaglandin G/H synthase 21.14.99.10.441
3r1rATPRibonucleoside-diphosphate reductase 1 subunit alpha1.17.4.10.441
3uhmRFNUDP-3-O-acyl-N-acetylglucosamine deacetylase/0.441
3zksWZVBeta-secretase 23.4.23.450.441
4bfvZVVPantothenate kinase2.7.1.330.441
4ih71ERGenome polyprotein2.7.7.480.441
4kc1WS1Histo-blood group ABO system transferase/0.441
5je3SAHMethyl transferase/0.441
5kj1PFBAlcohol dehydrogenase E chain1.1.1.10.441
1a80NDP2,5-diketo-D-gluconic acid reductase A1.1.1.3460.440
1cozCTPGlycerol-3-phosphate cytidylyltransferase2.7.7.390.440
1poxFADPyruvate oxidase1.2.3.30.440
2eerNADNAD-dependent alcohol dehydrogenase1.1.1.10.440
2h2aDNDProbable nicotinate-nucleotide adenylyltransferase/0.440
2zlaVDBVitamin D3 receptor/0.440
3gbuATPUncharacterized sugar kinase PH14592.7.10.440
3m31FADEndoplasmic oxidoreductin-11.8.40.440
3mjrAC2Deoxycytidine kinase2.7.1.740.440
3nx4NAPPutative oxidoreductase/0.440
3ske054Genome polyprotein2.7.7.480.440
4es5MGTPolymerase basic protein 2/0.440
4k3n1OTM17 leucyl aminopeptidase/0.440
4o7uTHFThymidylate synthase/0.440