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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
4ise1FWGlucokinase2.7.1.2

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
4ise1FWGlucokinase2.7.1.21.000
4isg1FYGlucokinase2.7.1.20.642
4isf1FXGlucokinase2.7.1.20.619
4dch4DCGlucokinase2.7.1.20.601
4dhyS41Glucokinase2.7.1.20.534
4mleVO1Glucokinase2.7.1.20.533
3h1vTK1Glucokinase2.7.1.20.518
3a0iAJIGlucokinase2.7.1.20.517
3imxB84Glucokinase2.7.1.20.508
3vev0H4Glucokinase2.7.1.20.504
3h3r14HCollagen type IV alpha-3-binding protein/0.494
3h3t16HCollagen type IV alpha-3-binding protein/0.490
1z6tADPApoptotic protease-activating factor 1/0.486
1fmlRTLRetinol dehydratase/0.485
2aouCQAHistamine N-methyltransferase2.1.1.80.485
3h3qH13Collagen type IV alpha-3-binding protein/0.485
4eufNADTrans-2-enoyl-CoA reductase [NADH]/0.481
1kkq471Peroxisome proliferator-activated receptor alpha/0.480
2e0nSAHPrecorrin-2 C20-methyltransferase/0.480
1dnpMHFDeoxyribodipyrimidine photo-lyase4.1.99.30.479
2hk9NAPShikimate dehydrogenase (NADP(+))/0.474
3pm1ETHTH-type transcriptional regulator QacR/0.474
4ixc1JDGlucokinase2.7.1.20.473
1a5bIGPTryptophan synthase alpha chain/0.470
2qimZEAClass 10 plant pathogenesis-related protein/0.470
4mlhVO2Glucokinase2.7.1.20.470
3dyqPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.469
3vey0H5Glucokinase2.7.1.20.469
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.468
2e8uIPEGeranylgeranyl pyrophosphate synthase/0.466
4iwv1J9Glucokinase2.7.1.20.466
1rdt570Peroxisome proliferator-activated receptor gamma/0.465
3id8MRKGlucokinase2.7.1.20.464
4v2gITCTetracycline repressor protein class D/0.464
4y9uNAPNADPH--cytochrome P450 reductase/0.464
1x8lOXRRetinol dehydratase/0.463
2vcmM11Isopenicillin N synthase1.21.3.10.463
3s41S41Glucokinase2.7.1.20.463
4nbb9CATerminal oxygenase component of carbazole/0.463
3a1cACPProbable copper-exporting P-type ATPase A3.6.3.540.462
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.462
4cdmFO1Deoxyribodipyrimidine photolyase/0.460
1nytNAPShikimate dehydrogenase (NADP(+))/0.458
1q0zAKAAclacinomycin methylesterase RdmC3.1.1.950.458
3c1oNAPEugenol synthase/0.458
3l6jZ90Alr2278 protein/0.458
3lpiZ74Beta-secretase 13.4.23.460.458
2rhrEMOPutative ketoacyl reductase1.3.10.457
4bfzZVZPantothenate kinase2.7.1.330.457
3h3sH15Collagen type IV alpha-3-binding protein/0.456
3nr4PYVAbscisic acid receptor PYL2/0.456
1dr3HBIDihydrofolate reductase1.5.1.30.455
1fx9MJIPhospholipase A2, major isoenzyme3.1.1.40.455
1q5dEPBEpothilone C/D epoxidase1.140.455
2yy2IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.455
3dopNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.455
3g5hYTTMycocyclosin synthase1.14.21.90.455
3phjDHKShikimate dehydrogenase (NADP(+))/0.455
4bfuZVUPantothenate kinase2.7.1.330.455
4k2xFADPolyketide oxygenase/hydroxylase/0.455
4bftZVTPantothenate kinase2.7.1.330.454
2wo7ASVIsopenicillin N synthase1.21.3.10.453
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.453
3zkyWT4Isopenicillin N synthase1.21.3.10.453
4iae1DXAlr2278 protein/0.453
1fmjRTLRetinol dehydratase/0.452
2jbsFMNp-hydroxyphenylacetate 3-hydroxylase, oxygenase component/0.452
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.452
3pn1IVHDNA ligase/0.452
4bfxZVXPantothenate kinase2.7.1.330.452
4dc0NDPPutative ketoacyl reductase1.3.10.452
4l3q926Glucokinase2.7.1.20.452
5cc9DDFDihydrofolate reductase1.5.1.30.452
1lf3EH5Plasmepsin-23.4.23.390.451
2a1hGBNBranched-chain-amino-acid aminotransferase, mitochondrial2.6.1.420.451
2hxzH7JCathepsin S3.4.22.270.451
2xviFADPutative flavin-containing monooxygenase/0.451
3dynPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.451
3dys5GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.451
3jyoNADQuinate/shikimate dehydrogenase (NAD(+))/0.451
3nxxNDPDihydrofolate reductase1.5.1.30.451
4iah1DXAlr2278 protein/0.451
1dr3TAPDihydrofolate reductase1.5.1.30.450
3lxiCAMCytochrome P450/0.450
4eph0RKCarnitine O-palmitoyltransferase 2, mitochondrial2.3.1.210.450
4g2l0WLHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.450
1kzjCB3Thymidylate synthase/0.449
1qjfACSIsopenicillin N synthase1.21.3.10.449
3h2sNDPPutative NADH-flavin reductase/0.449
3junAKDPhenazine biosynthesis protein A/B/0.449
3mpiFADGlutaryl-CoA dehydrogenase1.3.99.320.449
4ips1G4Mycocyclosin synthase1.14.21.90.449
1ps9MDE2,4-dienoyl-CoA reductase1.3.1.340.448
1vkgCRIHistone deacetylase 83.5.1.980.448
2a58RBF6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.448
2y6fM9FIsopenicillin N synthase1.21.3.10.448
3n39FMNProtein NrdI/0.448
4a83DXCMajor pollen allergen Bet v 1-A/0.448
4a8v2ANMajor pollen allergen Bet v 1-J/0.448
4b67NAPL-ornithine N(5)-monooxygenase/0.448
4bfvZVVPantothenate kinase2.7.1.330.448
4eu4COASuccinyl-CoA:acetate CoA-transferase/0.448
4k9oTPPBenzoylformate decarboxylase4.1.1.70.448
4yau2AMNADPH--cytochrome P450 reductase/0.448
2vtdLKMUDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.447
2zbaZBATrichothecene 3-O-acetyltransferase/0.447
3jypNADQuinate/shikimate dehydrogenase (NAD(+))/0.447
4bfwZVWPantothenate kinase2.7.1.330.447
4ktl1CQCytochrome P450/0.447
1nupNMNNicotinamide/nicotinic acid mononucleotide adenylyltransferase 3/0.446
3b9oFMNAlkane monoxygenase/0.446
3br3ETHTH-type transcriptional regulator QacR/0.446
3eheNADUDP-glucose 4-epimerase (GalE-1)/0.446
3g1rFIT3-oxo-5-beta-steroid 4-dehydrogenase/0.446
3sl2ATPSensor histidine kinase WalK/0.446
1p0pBCHCholinesterase3.1.1.80.445
1qoqIGPTryptophan synthase alpha chain/0.445
2uxuNARHTH-type transcriptional regulator TtgR/0.445
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.445
3m1vCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.445
3m1vCOMMethyl-coenzyme M reductase I subunit beta2.8.4.10.445
1cjkFOKAdenylate cyclase type 2/0.444
1cjkFOKAdenylate cyclase type 5/0.444
1oc1ASVIsopenicillin N synthase1.21.3.10.444
2ejvNADL-threonine 3-dehydrogenase/0.444
2gjlFMNNitronate monooxygenase1.13.12.160.444
3fznD7KBenzoylformate decarboxylase4.1.1.70.444
3lkhLT6Genome polyprotein2.7.7.480.444
4bfyZVYPantothenate kinase2.7.1.330.444
4fhf0TTSpore photoproduct lyase/0.444
1cf3FADGlucose oxidase1.1.3.40.443
1i5rHYCEstradiol 17-beta-dehydrogenase 11.1.1.620.443
2j2pSC2Ficolin-2/0.443
2rqfJH3Hemolymph juvenile hormone binding protein/0.443
3i2834NBifunctional epoxide hydrolase 23.3.2.100.443
3uzxAOX3-oxo-5-beta-steroid 4-dehydrogenase/0.443
3v1s0LHStrictosidine synthase4.3.3.20.443
3nyaJTZBeta-2 adrenergic receptor/0.443
1gj4132Prothrombin3.4.21.50.442
1qiqACCIsopenicillin N synthase1.21.3.10.442
2a5kAZPReplicase polyprotein 1ab3.4.220.442
2pobGW4Peroxisome proliferator-activated receptor gamma/0.442
2uxoTACHTH-type transcriptional regulator TtgR/0.442
2xiq5ADMethylmalonyl-CoA mutase, mitochondrial/0.442
3ou2SAHSAM-dependent methyltransferase/0.442
4g1z0VPVitamin D3 receptor A/0.442
4qnuGEKtRNA U34 carboxymethyltransferase/0.442
1aquESTEstrogen sulfotransferase, testis isoform2.8.2.40.441
1c7oPPGHemolysin/0.441
1t7o152Carnitine O-acetyltransferase2.3.1.70.441
2cy0NAPShikimate dehydrogenase (NADP(+))/0.441
2ov2GCPRas-related C3 botulinum toxin substrate 3/0.441
2wqpWQPPolysialic acid capsule biosynthesis protein SiaC/0.441
2y60M8FIsopenicillin N synthase1.21.3.10.441
4c3yFAD3-ketosteroid dehydrogenase/0.441
4g2j0WFHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
4req5ADMethylmalonyl-CoA mutase large subunit5.4.99.20.441
4y9rNAPNADPH--cytochrome P450 reductase/0.441
1x7gNAPPutative ketoacyl reductase1.3.10.440
2ij7TPFMycocyclosin synthase1.14.21.90.440
2nr4FMNConserved protein/0.440
2zevIPEGeranylgeranyl pyrophosphate synthase/0.440
3bv7NAP3-oxo-5-beta-steroid 4-dehydrogenase/0.440
3c15FOKAdenylate cyclase type 2/0.440
3c15FOKAdenylate cyclase type 5/0.440
3sgv2BJDitrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.440
4b66NAPL-ornithine N(5)-monooxygenase/0.440
4ho6UTPGlucose-1-phosphate thymidylyltransferase/0.440
4mr92BXGamma-aminobutyric acid type B receptor subunit 1/0.440