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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Cavity similarities measured by Shaper
You can zoom onto the graph by using the mouse to make a selection

Cavities 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

Reference Protein Data Bank Entry :
PDB ID HET Uniprot Name EC Number
4f1q0RZPoly [ADP-ribose] polymerase 142.4.2.30

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
4f1q0RZPoly [ADP-ribose] polymerase 142.4.2.301.000
4gv08MEPoly [ADP-ribose] polymerase 32.4.2.300.546
1paxDHQPoly [ADP-ribose] polymerase 12.4.2.300.538
3ce0P34Poly [ADP-ribose] polymerase 32.4.2.300.538
1efyBZCPoly [ADP-ribose] polymerase 12.4.2.300.529
3c4hDRLPoly [ADP-ribose] polymerase 32.4.2.300.525
4bjcRPBTankyrase-22.4.2.300.523
4tjy3GNTankyrase-22.4.2.300.522
2rcwAAIPoly [ADP-ribose] polymerase 12.4.2.300.521
5ds309LPoly [ADP-ribose] polymerase 12.4.2.300.520
2hxzH7JCathepsin S3.4.22.270.519
3l3lL3LPoly [ADP-ribose] polymerase 12.4.2.300.516
4l6s1WQPoly [ADP-ribose] polymerase 12.4.2.300.516
4bjbP34Tankyrase-22.4.2.300.513
3exfTPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial1.2.4.10.512
3exfTPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial1.2.4.10.512
4hhy15RPoly [ADP-ribose] polymerase 12.4.2.300.512
3c49KU8Poly [ADP-ribose] polymerase 32.4.2.300.511
1ikgREXD-alanyl-D-alanine carboxypeptidase3.4.16.40.510
3gjwGJWPoly [ADP-ribose] polymerase 12.4.2.300.510
4hhz15SPoly [ADP-ribose] polymerase 12.4.2.300.510
1ni4TPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial1.2.4.10.505
1ni4TPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial1.2.4.10.505
4r5wXAVPoly [ADP-ribose] polymerase 12.4.2.300.505
2rd678PPoly [ADP-ribose] polymerase 12.4.2.300.502
3l3mA92Poly [ADP-ribose] polymerase 12.4.2.300.499
3nubUD0UDP-2-acetamido-2-deoxy-3-oxo-D-glucuronate aminotransferase2.6.1.980.497
3fr5I4AFatty acid-binding protein, adipocyte/0.495
3dopNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.493
4gtm7TMProtein farnesyltransferase subunit beta2.5.1.580.493
1frbZSTAldose reductase-related protein 2/0.492
2jl1NAPTriphenylmethane reductase/0.491
3gn73GNPoly [ADP-ribose] polymerase 12.4.2.300.490
3mauPLRPutative sphingosine-1-phosphate lyase/0.487
1uk0FRMPoly [ADP-ribose] polymerase 12.4.2.300.486
3hdyGDUUDP-galactopyranose mutase/0.484
5dsyUHBPoly [ADP-ribose] polymerase 22.4.2.300.482
3r7mSUZAldo-keto reductase family 1 member C3/0.481
1towCRZFatty acid-binding protein, adipocyte/0.479
4bftZVTPantothenate kinase2.7.1.330.475
1mlzPLPAdenosylmethionine-8-amino-7-oxononanoate aminotransferase2.6.1.620.473
3fznD7KBenzoylformate decarboxylase4.1.1.70.473
4gv7MEWPoly [ADP-ribose] polymerase 12.4.2.300.473
1bx1FADFerredoxin--NADP reductase, chloroplastic1.18.1.20.472
1s7gNADNAD-dependent protein deacylase 2/0.472
3geyP34Poly [ADP-ribose] polymerase 152.4.2.300.472
3mhpFADFerredoxin--NADP reductase, leaf isozyme, chloroplastic1.18.1.20.472
3r6iJMSAldo-keto reductase family 1 member C3/0.472
3g1rNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.471
4n4t2GVTankyrase-12.4.2.300.471
2a58RBF6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.470
2aq7TL53-oxoacyl-[acyl-carrier-protein] synthase 12.3.1.410.470
2ym1FADPhenylacetone monooxygenase1.14.13.920.470
4ey6GNTAcetylcholinesterase3.1.1.70.469
1rkwPNTHTH-type transcriptional regulator QacR/0.468
1xzqFONtRNA modification GTPase MnmE3.6.50.468
2cekN8TAcetylcholinesterase3.1.1.70.468
3br3ETHTH-type transcriptional regulator QacR/0.467
1kbo340NAD(P)H dehydrogenase [quinone] 11.6.5.20.466
2vt4P32Beta-1 adrenergic receptor/0.466
3fr4F8AFatty acid-binding protein, adipocyte/0.466
1a26CNAPoly [ADP-ribose] polymerase 12.4.2.300.465
1fapRAPPeptidyl-prolyl cis-trans isomerase FKBP1A5.2.1.80.465
1fapRAPSerine/threonine-protein kinase mTOR2.7.11.10.465
3imxB84Glucokinase2.7.1.20.464
1typNAPTrypanothione reductase1.8.1.120.463
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.463
3qgi33FGenome polyprotein2.7.7.480.463
4kdrSAHUbiquinone biosynthesis O-methyltransferase/0.463
1touB1VFatty acid-binding protein, adipocyte/0.461
3o73O73Ribosyldihydronicotinamide dehydrogenase [quinone]/0.461
4hlm16STankyrase-22.4.2.300.461
2rc6FADFerredoxin--NADP reductase/0.460
3owxXRARibosyldihydronicotinamide dehydrogenase [quinone]/0.460
3pz3PZ3Geranylgeranyl transferase type-2 subunit beta2.5.1.600.460
4bfxZVXPantothenate kinase2.7.1.330.460
1bwlFMNNADPH dehydrogenase 11.6.99.10.459
1w19T1P6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.459
2wzySQXSoluble acetylcholine receptor/0.459
3r8gIZPAldo-keto reductase family 1 member C3/0.459
1gpnHUBAcetylcholinesterase3.1.1.70.458
1odcA8BAcetylcholinesterase3.1.1.70.458
2vb8TLM3-oxoacyl-[acyl-carrier-protein] synthase 12.3.1.410.458
4fhd0TTSpore photoproduct lyase/0.458
4jtrIZPAldo-keto reductase family 1 member C2/0.458
2gevCOKPantothenate kinase2.7.1.330.457
3sqxANPATP-dependent RNA helicase MSS116, mitochondrial3.6.4.130.457
4l321VFTankyrase-22.4.2.300.457
1yciNDFHypoxia-inducible factor 1-alpha inhibitor1.14.11.300.456
1zm4TADExotoxin A2.4.2.360.456
2pksG44Prothrombin3.4.21.50.456
1fnbFADFerredoxin--NADP reductase, chloroplastic1.18.1.20.455
1t7o152Carnitine O-acetyltransferase2.3.1.70.455
4b63NAPL-ornithine N(5)-monooxygenase/0.455
5d7qAR6NAD-dependent protein deacetylase sirtuin-23.5.10.455
1gt5BZQOdorant-binding protein/0.454
1kyxCRM6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.454
1mrqSTRAldo-keto reductase family 1 member C1/0.454
1pw1HELD-alanyl-D-alanine carboxypeptidase3.4.16.40.454
1uscFMNMonooxygenase/0.454
2jh5895Prothrombin3.4.21.50.454
2x6o2TCTetracycline repressor protein class D/0.454
3tpr5HABeta-secretase 13.4.23.460.454
1azlFMNFlavodoxin/0.453
1u2rSO1Elongation factor 2/0.453
1xi2CB1Ribosyldihydronicotinamide dehydrogenase [quinone]/0.453
3cvkN34Genome polyprotein2.7.7.480.453
3ox279XRibosyldihydronicotinamide dehydrogenase [quinone]/0.453
4gz612VUDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit/0.453
4jpg1OXPyruvate kinase PKM2.7.1.400.453
1el4CTZObelin/0.452
1gpuTHDTransketolase 12.2.1.10.452
1mu6CDAProthrombin3.4.21.50.452
2fhkMFNFormylmethanofuran--tetrahydromethanopterin formyltransferase2.3.1.1010.452
4hej14DThymidylate kinase/0.452
4zu44TGWxcM-like protein/0.452
3d4sTIMBeta-2 adrenergic receptor/0.452
1opmIYGPeptidyl-glycine alpha-amidating monooxygenase1.14.17.30.451
2qw8NAPEugenol synthase 11.1.1.3180.451
2tohHBITyrosine 3-monooxygenase1.14.16.20.451
3c1oNAPEugenol synthase/0.451
3hxdBD7Geranylgeranyl transferase type-2 subunit beta2.5.1.600.451
4c77N01Phenylacetone monooxygenase1.14.13.920.451
5a4vQUEGlutathione S-transferase F22.5.1.180.451
1ut6A8NAcetylcholinesterase3.1.1.70.450
2geuCOKPantothenate kinase2.7.1.330.450
2ha6SCKAcetylcholinesterase3.1.1.70.450
3b8xG4MPutative pyridoxamine 5-phosphate-dependent dehydrase/0.450
3fhxPLPPyridoxal kinase2.7.1.350.450
3g5iDNBPyrimidine-specific ribonucleoside hydrolase RihA/0.450
4af7FADFerredoxin--NADP reductase, leaf isozyme, chloroplastic1.18.1.20.450
4b4w9L9Bifunctional protein FolD/0.450
4fa30SLAldo-keto reductase family 1 member C3/0.450
5choFADFlavin reductase/0.450
1oj4CDM4-diphosphocytidyl-2-C-methyl-D-erythritol kinase2.7.1.1480.449
2e8hSAHDiphthine synthase/0.449
2ed5SAHDiphthine synthase/0.449
3c3xNAPEugenol synthase 11.1.1.3180.449
3frkTQPQdtB/0.449
3fsjD7KBenzoylformate decarboxylase4.1.1.70.449
3n3zIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.449
3uaxNOSPurine nucleoside phosphorylase DeoD-type/0.449
4eplJAIJasmonic acid-amido synthetase JAR16.3.20.449
1gw2FERPeroxidase C1A1.11.1.70.448
1mczRMNBenzoylformate decarboxylase4.1.1.70.448
1queFADFerredoxin--NADP reductase1.18.1.20.448
2dshSAHDiphthine synthase/0.448
2xlpFADPutative flavin-containing monooxygenase/0.448
4jq4IMNAldo-keto reductase family 1 member C2/0.448
4ms1381Gamma-aminobutyric acid type B receptor subunit 1/0.448
1rftPXMPyridoxal kinase2.7.1.350.447
1thz326Bifunctional purine biosynthesis protein PURH2.1.2.30.447
2abaSTRPentaerythritol tetranitrate reductase/0.447
2b8jADNClass B acid phosphatase3.1.3.20.447
3iktNADRedox-sensing transcriptional repressor Rex/0.447
3jqrFADFerredoxin--NADP reductase, apicoplast/0.447
4b5nFMNNAD(P)H:flavin oxidoreductase Sye4/0.447
4zqcF6FTryptophan synthase alpha chain/0.447
1g1dFSBCarbonic anhydrase 24.2.1.10.446
1gky5GPGuanylate kinase2.7.4.80.446
1pq944BOxysterols receptor LXR-beta/0.446
1zq5E04Aldo-keto reductase family 1 member C3/0.446
2dsgSAHDiphthine synthase/0.446
2uagUMAUDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.446
3k2fNKXCarbonic anhydrase 24.2.1.10.446
3ox34X4Ribosyldihydronicotinamide dehydrogenase [quinone]/0.446
3w6uNAP6-phosphogluconate dehydrogenase, NAD-binding protein/0.446
3zj7C1KStrictosidine-O-beta-D-glucosidase3.2.1.1050.446
4i6h1C8Serine/threonine-protein kinase PLK22.7.11.210.446
4isf1FXGlucokinase2.7.1.20.446
1po7TZDBenzoylformate decarboxylase4.1.1.70.445
1umcTDP2-oxoisovalerate dehydrogenase subunit alpha1.2.4.40.445
1umcTDP2-oxoisovalerate dehydrogenase subunit beta1.2.4.40.445
1xq04TRCarbonic anhydrase 24.2.1.10.445
2a59LMZ6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.445
2c6c24IGlutamate carboxypeptidase 23.4.17.210.445
2ipiAKYAclacinomycin-N/aclacinomycin-A oxidase/0.445
3eu5GBOProtein farnesyltransferase subunit beta2.5.1.580.445
3pce3HPProtocatechuate 3,4-dioxygenase alpha chain1.13.11.30.445
3pce3HPProtocatechuate 3,4-dioxygenase beta chain1.13.11.30.445
3pm1ETHTH-type transcriptional regulator QacR/0.445
3zj6VM2Raucaffricine-O-beta-D-glucosidase3.2.1.1250.445
1ngsTPPTransketolase 12.2.1.10.444
2dv4SAHDiphthine synthase/0.444
2fjeFADAdenylylsulfate reductase, subunit A (AprA)/0.444
2uuk897Prothrombin3.4.21.50.444
2zhf49UProthrombin3.4.21.50.444
3n3jWWVCarbonic anhydrase 24.2.1.10.444
3vo2FADFerredoxin--NADP reductase/0.444
4isg1FYGlucokinase2.7.1.20.444
4j1k1HGBeta-secretase 13.4.23.460.444
4je5PLPAromatic/aminoadipate aminotransferase 12.6.1.390.444
5ahsCOAAcyl-CoA dehydrogenase/0.444
3vw7VPXProteinase-activated receptor 1/0.444
1kquBR4Phospholipase A2, membrane associated/0.443
1rpwDIDHTH-type transcriptional regulator QacR/0.443
1uk1FRQPoly [ADP-ribose] polymerase 12.4.2.300.443
2xuhTZ4Acetylcholinesterase3.1.1.70.443
3b4yF42F420-dependent glucose-6-phosphate dehydrogenase/0.443
4cjx9L9C-1-tetrahydrofolate synthase, cytoplasmic, putative/0.443
4h8i11WGlutamate receptor ionotropic, kainate 2/0.443
4qtnNNRNicotinamide riboside transporter PnuC/0.443
4uugPXGBranched-chain amino acid aminotransferase, putative/0.443
4xo7ASDAldo-keto reductase family 1 member C2/0.443
4u163C0Muscarinic acetylcholine receptor M3/0.443
1kw9BPYBiphenyl-2,3-diol 1,2-dioxygenase1.13.11.390.442
1t3zCAOFormyl-CoA:oxalate CoA-transferase/0.442
2wcgMT5Glucosylceramidase3.2.1.450.442
3e32ED2Protein farnesyltransferase subunit beta2.5.1.580.442
3h3r14HCollagen type IV alpha-3-binding protein/0.442
3hxfBD9Geranylgeranyl transferase type-2 subunit beta2.5.1.600.442
3nhjA2ZRibosyldihydronicotinamide dehydrogenase [quinone]/0.442
3zg6APRNAD-dependent protein deacetylase sirtuin-63.5.10.442
1k7fIAVTryptophan synthase alpha chain/0.441
1qoqIGPTryptophan synthase alpha chain/0.441
1ttm667Carbonic anhydrase 24.2.1.10.441
1xk9P34Exotoxin A2.4.2.360.441
2j3qTFLAcetylcholinesterase3.1.1.70.441
2uxoTACHTH-type transcriptional regulator TtgR/0.441
3d3p20AcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.441
3h59H59Genome polyprotein2.7.7.480.441
3nhpHGZRibosyldihydronicotinamide dehydrogenase [quinone]/0.441
4bfuZVUPantothenate kinase2.7.1.330.441
4cf6CBDNAD(P)H dehydrogenase [quinone] 11.6.5.20.441
4n4v2GYTankyrase-12.4.2.300.441
2cicDUPDUTPase/0.440
2egbSAHDiphthine synthase/0.440
2pzjNADPutative nucleotide sugar epimerase/ dehydratase/0.440
3c72CX1Geranylgeranyl transferase type-2 subunit beta2.5.1.600.440
3hmvHBTcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.440
3nxvD2FDihydrofolate reductase1.5.1.30.440
3qwc98PProthrombin3.4.21.50.440
3rtnRTNBeta-secretase 13.4.23.460.440
3w2fNADNADH-cytochrome b5 reductase 31.6.2.20.440
3zpqXF5Beta-1 adrenergic receptor/0.440
4dbw511Aldo-keto reductase family 1 member C3/0.440
4eywL0RCarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.440
4gi2NAPCrotonyl-CoA carboxylase/reductase/0.440
4u0zAPCAdenosine monophosphate-protein transferase FICD2.7.7.n10.440