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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
1ndcTYDNucleoside diphosphate kinase, cytosolic2.7.4.6

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
1ndcTYDNucleoside diphosphate kinase, cytosolic2.7.4.61.000
1buxPPSNucleoside diphosphate kinase, cytosolic2.7.4.60.557
1nhkCMPNucleoside diphosphate kinase2.7.4.60.549
3nguADPNucleoside diphosphate kinase/0.539
3q8uADPNucleoside diphosphate kinase/0.533
1wklATPNucleoside diphosphate kinase/0.516
4uohADPNucleoside diphosphate kinase/0.516
1zs6ADPNucleoside diphosphate kinase 32.7.4.60.511
1lwxAZDNucleoside diphosphate kinase, cytosolic2.7.4.60.500
2dxdANPNucleoside diphosphate kinase2.7.4.60.500
4u0mGTPCyclic GMP-AMP synthase/0.495
2az3CDPNucleoside diphosphate kinase/0.494
4fkxCDPNucleoside diphosphate kinase/0.494
3keuATPPyridoxal kinase2.7.1.350.492
2hveADPNucleoside diphosphate kinase A2.7.4.60.489
4uogYYYNucleoside diphosphate kinase/0.489
1dfoFFOSerine hydroxymethyltransferase2.1.2.10.488
4hr2ADPNucleoside diphosphate kinase/0.487
4dpy2P0Mevalonate diphosphate decarboxylase/0.486
4hbm0Y7E3 ubiquitin-protein ligase Mdm26.3.20.483
2dxfGNPNucleoside diphosphate kinase2.7.4.60.482
1u1d181Uridine phosphorylase2.4.2.30.480
2hvdADPNucleoside diphosphate kinase A2.7.4.60.478
4b5nFMNNAD(P)H:flavin oxidoreductase Sye4/0.470
4k3n1OTM17 leucyl aminopeptidase/0.470
4uofDATNucleoside diphosphate kinase/0.469
3fbcTYDNucleoside diphosphate kinase2.7.4.60.467
4wdb2AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.466
2o6hINI6,7-dimethyl-8-ribityllumazine synthase 12.5.1.780.465
4bb3KKAIsopenicillin N synthase1.21.3.10.464
3zbsOVE2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.462
1be4PCGNucleoside diphosphate kinase A 22.7.4.60.461
1nueGDPNucleoside diphosphate kinase B2.7.4.60.459
3ituIBMcGMP-dependent 3',5'-cyclic phosphodiesterase3.1.4.170.459
2dy9ADPNucleoside diphosphate kinase2.7.4.60.458
4u0zAPCAdenosine monophosphate-protein transferase FICD2.7.7.n10.458
4ge40KEKynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.457
1kqwRTLCellular retinol-binding protein type II/0.456
1rfvADPPyridoxal kinase2.7.1.350.455
3aezGDPPantothenate kinase2.7.1.330.455
3hdqGDUUDP-galactopyranose mutase/0.455
3zbzOVE2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.455
2ydoADNAdenosine receptor A2a/0.454
3havATPAminoglycoside phosphotransferase/0.454
3vv8B02Beta-secretase 13.4.23.460.454
4qi5FADCellobiose dehydrogenase/0.454
4u0sADPAdenosine monophosphate-protein transferase FICD2.7.7.n10.454
3slkNDPPolyketide synthase extender module 2/0.453
5f54TMPSingle-stranded-DNA-specific exonuclease/0.453
2xvw9NRSerum albumin/0.452
3i0pNADMalate dehydrogenase, putative/0.452
1e8zSTUPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.451
1u1cBAUUridine phosphorylase2.4.2.30.451
2b7aIZATyrosine-protein kinase JAK2/0.451
3gieACPSensor histidine kinase DesK2.7.13.30.451
3zkyWT4Isopenicillin N synthase1.21.3.10.451
4iaq2GM5-hydroxytryptamine receptor 1B/0.451
1mrqSTRAldo-keto reductase family 1 member C1/0.448
3qi4IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.448
2xckMH43-phosphoinositide-dependent protein kinase 12.7.11.10.447
3b9lAZZSerum albumin/0.447
3cgbCOACoenzyme A disulfide reductase/0.447
2dvlFADAcyl-CoA dehydrogenase/0.446
2yq92AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.446
4j531J4Serine/threonine-protein kinase PLK12.7.11.210.446
1o04NADAldehyde dehydrogenase, mitochondrial1.2.1.30.445
1rp4FADEndoplasmic oxidoreductin-11.8.40.445
2yozOVE2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.445
2zshGA3Gibberellin receptor GID1A30.445
3zknWZVBeta-secretase 23.4.23.450.445
5kghACOPredicted acetyltransferase/0.445
5kgpACOPredicted acetyltransferase/0.445
1dgfNDPCatalase1.11.1.60.444
3jzdNADMaleylacetate reductase/0.444
4isk1JYThymidylate synthase/0.444
4rphGDUUDP-galactopyranose mutase5.4.99.90.444
5iqdGNPBifunctional AAC/APH2.3.10.444
2geuCOKPantothenate kinase2.7.1.330.443
3hk1B64Fatty acid-binding protein, adipocyte/0.443
3tfjTHGDimethylsulfonioproprionate demethylase DmdA2.1.1.2690.443
1sze173Cytochrome b2, mitochondrial1.1.2.30.442
2ydbNAP2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.442
5a88ADPRiboflavin biosynthesis protein RibF2.7.1.260.442
5iotUMPFlavin-dependent thymidylate synthase2.1.1.1480.442
1bsvNDPGDP-L-fucose synthase/0.441
4dpuAGSMevalonate diphosphate decarboxylase/0.441
2w02ATPAcsD/0.440
2xvv9DNSerum albumin/0.440
3rn8RN8Glutamate receptor 2/0.440
4g2l0WLHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440