sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
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
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 4gda | BTN | Streptavidin |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4gda | BTN | Streptavidin | / | 1.000 | |
| 3ry2 | BTN | Streptavidin | / | 0.664 | |
| 2rtg | BTN | Streptavidin | / | 0.631 | |
| 1srg | MHB | Streptavidin | / | 0.623 | |
| 4bx7 | B4F | Streptavidin | / | 0.621 | |
| 2izf | BTN | Streptavidin | / | 0.618 | |
| 2rti | GLL | Streptavidin | / | 0.615 | |
| 2rtn | IMI | Streptavidin | / | 0.615 | |
| 1sre | HAB | Streptavidin | / | 0.610 | |
| 1stp | BTN | Streptavidin | / | 0.610 | |
| 1lcw | SHM | Streptavidin | / | 0.607 | |
| 2rte | BTN | Streptavidin | / | 0.604 | |
| 2izg | BTN | Streptavidin | / | 0.603 | |
| 2izl | IMI | Streptavidin | / | 0.602 | |
| 2izh | BTN | Streptavidin | / | 0.600 | |
| 1mk5 | BTN | Streptavidin | / | 0.599 | |
| 2izk | GLL | Streptavidin | / | 0.598 | |
| 2rto | IMI | Streptavidin | / | 0.598 | |
| 2rtd | BTN | Streptavidin | / | 0.597 | |
| 2rtf | BTN | Streptavidin | / | 0.594 | |
| 1rxh | BNI | Streptavidin | / | 0.592 | |
| 4dne | DTB | Streptavidin | / | 0.591 | |
| 1lcz | BH7 | Streptavidin | / | 0.588 | |
| 1srj | NAB | Streptavidin | / | 0.585 | |
| 2rtp | IMI | Streptavidin | / | 0.585 | |
| 1i9h | BNI | Streptavidin | / | 0.584 | |
| 3wzn | BTN | Streptavidin | / | 0.584 | |
| 1sri | DMB | Streptavidin | / | 0.579 | |
| 2fhl | BNI | Avidin-related protein 4/5 | / | 0.578 | |
| 2y3f | BTN | Streptavidin | / | 0.578 | |
| 1swt | BTN | Streptavidin | / | 0.576 | |
| 2rtk | GLL | Streptavidin | / | 0.576 | |
| 2rtq | IMI | Streptavidin | / | 0.576 | |
| 2avi | BTN | Avidin | / | 0.575 | |
| 3wyq | BTN | Streptavidin | / | 0.574 | |
| 1srf | MTB | Streptavidin | / | 0.567 | |
| 1df8 | BTN | Streptavidin | / | 0.562 | |
| 1luq | BTN | Streptavidin | / | 0.562 | |
| 1y52 | BTN | Avidin-related protein 4/5 | / | 0.561 | |
| 2uyw | BTN | Avd protein | / | 0.558 | |
| 4bcs | BTN | Avidin-related protein 4/5 | / | 0.556 | |
| 1srh | MOB | Streptavidin | / | 0.555 | |
| 2fhn | BNI | Avidin-related protein 4/5 | / | 0.554 | |
| 2c4i | BTN | Avidin | / | 0.551 | |
| 3rdq | DTB | Streptavidin | / | 0.551 | |
| 4z28 | BTN | Hoefavidin | / | 0.547 | |
| 2izi | BTN | Streptavidin | / | 0.546 | |
| 2izj | BTN | Streptavidin | / | 0.544 | |
| 2rtr | IMI | Streptavidin | / | 0.541 | |
| 1avd | BTN | Avidin | / | 0.533 | |
| 3ew2 | BTN | Hypothetical conserved protein | / | 0.532 | |
| 2rtm | IMI | Streptavidin | / | 0.523 | |
| 1nc9 | IMI | Streptavidin | / | 0.519 | |
| 2uz2 | BTN | Avd protein | / | 0.512 | |
| 3t2w | BTN | Avidin/streptavidin | / | 0.502 | |
| 1swp | BTQ | Streptavidin | / | 0.494 | |
| 2a5c | 8DA | Avidin | / | 0.492 | |
| 3h3r | 14H | Collagen type IV alpha-3-binding protein | / | 0.489 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.488 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.488 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.488 | |
| 2rtl | IMI | Streptavidin | / | 0.485 | |
| 4psb | GA3 | Cytokinin-specific binding protein | / | 0.484 | |
| 4abk | AR6 | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.483 | |
| 1b3d | S27 | Stromelysin-1 | 3.4.24.17 | 0.482 | |
| 2y6f | M9F | Isopenicillin N synthase | 1.21.3.1 | 0.481 | |
| 3c3x | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.479 | |
| 2flh | ZEA | Cytokinin-specific binding protein | / | 0.477 | |
| 2zba | ZBA | Trichothecene 3-O-acetyltransferase | / | 0.477 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.477 | |
| 1piw | NAP | NADP-dependent alcohol dehydrogenase 6 | 1.1.1.2 | 0.476 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.476 | |
| 1ndj | BTN | Streptavidin | / | 0.475 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.474 | |
| 3bk2 | U5P | Ribonuclease J | / | 0.472 | |
| 3h3s | H15 | Collagen type IV alpha-3-binding protein | / | 0.469 | |
| 3up3 | XCA | aceDAF-12 | / | 0.469 | |
| 3uxv | GUN | NADPH-dependent 7-cyano-7-deazaguanine reductase | / | 0.469 | |
| 1mvs | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.468 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.467 | |
| 1c3x | 8IG | Purine nucleoside phosphorylase | 2.4.2.1 | 0.465 | |
| 1r2j | FAD | FkbI | / | 0.465 | |
| 2zjw | REF | Casein kinase II subunit alpha | 2.7.11.1 | 0.465 | |
| 2npf | MOU | Elongation factor 2 | / | 0.464 | |
| 2toh | HBI | Tyrosine 3-monooxygenase | 1.14.16.2 | 0.464 | |
| 3uax | NOS | Purine nucleoside phosphorylase DeoD-type | / | 0.464 | |
| 1kt6 | RTL | Retinol-binding protein 4 | / | 0.463 | |
| 2gvd | FKP | Adenylate cyclase type 2 | / | 0.463 | |
| 2gvd | FKP | Adenylate cyclase type 5 | / | 0.463 | |
| 4gd9 | BTN | Streptavidin | / | 0.463 | |
| 3sn6 | P0G | Beta-2 adrenergic receptor | / | 0.463 | |
| 1pd9 | CO4 | Dihydrofolate reductase | 1.5.1.3 | 0.462 | |
| 3eks | CY9 | Actin-5C | / | 0.461 | |
| 4bj8 | BTN | Avidin | / | 0.461 | |
| 4rn6 | 15U | Prothrombin | 3.4.21.5 | 0.461 | |
| 4xd1 | T3Q | Qdtf | / | 0.461 | |
| 2pks | G44 | Prothrombin | 3.4.21.5 | 0.460 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.460 | |
| 1qyx | ASD | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.459 | |
| 1hdo | NAP | Flavin reductase (NADPH) | / | 0.458 | |
| 1rsz | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.458 | |
| 4fxy | 0W2 | Neurolysin, mitochondrial | 3.4.24.16 | 0.458 | |
| 2h2q | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.457 | |
| 1kt7 | RTL | Retinol-binding protein 4 | / | 0.456 | |
| 2bu9 | HFV | Isopenicillin N synthase | 1.21.3.1 | 0.456 | |
| 4du8 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.456 | |
| 4fc7 | NAP | Peroxisomal 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.456 | |
| 4gev | CB3 | Thymidylate synthase | / | 0.456 | |
| 1mvt | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.455 | |
| 1rt9 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.455 | |
| 2jgs | BTN | Avidin | / | 0.455 | |
| 2o1x | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.455 | |
| 3maa | FKP | Adenylate cyclase type 2 | / | 0.455 | |
| 3maa | FKP | Adenylate cyclase type 5 | / | 0.455 | |
| 1qf4 | RPD | Adenylosuccinate synthetase | / | 0.454 | |
| 1uxj | NAD | Malate dehydrogenase | / | 0.454 | |
| 1uzw | CDH | Isopenicillin N synthase | 1.21.3.1 | 0.454 | |
| 2ji9 | TPW | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.454 | |
| 2y1o | T26 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.454 | |
| 4dpe | NGH | Stromelysin-1 | 3.4.24.17 | 0.454 | |
| 4z1f | H71 | Heat shock protein 75 kDa, mitochondrial | / | 0.454 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 2w6o | OA3 | Biotin carboxylase | 6.3.4.14 | 0.453 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.453 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 4a81 | DXC | Major pollen allergen Bet v 1-A | / | 0.453 | |
| 4ja1 | NGH | Stromelysin-1 | 3.4.24.17 | 0.453 | |
| 4kfq | KFQ | Glutamate receptor ionotropic, NMDA 1 | / | 0.453 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.453 | |
| 2wns | OMP | Uridine 5'-monophosphate synthase | 2.4.2.10 | 0.452 | |
| 2y60 | M8F | Isopenicillin N synthase | 1.21.3.1 | 0.452 | |
| 1dr3 | TAP | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 1lke | DOG | Bilin-binding protein | / | 0.451 | |
| 1trg | CB3 | Thymidylate synthase | / | 0.451 | |
| 2qo6 | CHD | Fatty acid-binding protein 10-A, liver basic | / | 0.451 | |
| 3ch6 | 311 | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.451 | |
| 3fhx | PXL | Pyridoxal kinase | 2.7.1.35 | 0.451 | |
| 3pah | XDE | Phenylalanine-4-hydroxylase | 1.14.16.1 | 0.451 | |
| 4f4d | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.451 | |
| 4l4x | NDP | AmphI | / | 0.451 | |
| 5ai5 | BSU | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.451 | |
| 5cmx | 0G6 | Prothrombin | 3.4.21.5 | 0.451 | |
| 1d8f | SPI | Stromelysin-1 | 3.4.24.17 | 0.450 | |
| 2cbr | A80 | Cellular retinoic acid-binding protein 1 | / | 0.450 | |
| 2imp | NAI | Lactaldehyde dehydrogenase | 1.2.1.22 | 0.450 | |
| 3h3t | 16H | Collagen type IV alpha-3-binding protein | / | 0.450 | |
| 4a8v | 2AN | Major pollen allergen Bet v 1-J | / | 0.450 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.450 | |
| 4kp7 | 1UQ | 1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic | 1.1.1.267 | 0.450 | |
| 4pah | LNR | Phenylalanine-4-hydroxylase | 1.14.16.1 | 0.450 | |
| 1ia1 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.449 | |
| 1ikg | REX | D-alanyl-D-alanine carboxypeptidase | 3.4.16.4 | 0.449 | |
| 2h94 | FAD | Lysine-specific histone demethylase 1A | 1 | 0.449 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial | 1.2.4.4 | 0.449 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial | 1.2.4.4 | 0.449 | |
| 4dz7 | D02 | Carbonic anhydrase 2 | 4.2.1.1 | 0.449 | |
| 4fqs | LYA | Thymidylate synthase ThyA | / | 0.449 | |
| 4qzu | RTL | Retinol-binding protein 2 | / | 0.449 | |
| 4wh2 | ADP | N-acetylhexosamine 1-kinase | 2.7.1.162 | 0.449 | |
| 1f8g | NAD | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.448 | |
| 1rf7 | DHF | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 2hdj | NDP | Aldo-keto reductase family 1 member C2 | / | 0.448 | |
| 3wyp | BSO | Streptavidin | / | 0.448 | |
| 4m83 | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.448 | |
| 1axw | MTX | Thymidylate synthase | / | 0.447 | |
| 1dfo | PLG | Serine hydroxymethyltransferase | 2.1.2.1 | 0.447 | |
| 1j49 | NAD | D-lactate dehydrogenase | 1.1.1.28 | 0.447 | |
| 1m78 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 1ni4 | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.447 | |
| 1ni4 | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.447 | |
| 1psa | 0ZL | Pepsin A | 3.4.23.1 | 0.447 | |
| 1s3u | TQD | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 2hve | ADP | Nucleoside diphosphate kinase A | 2.7.4.6 | 0.447 | |
| 2z52 | H23 | Geranylgeranyl pyrophosphate synthase | / | 0.447 | |
| 3el7 | PD3 | Proto-oncogene tyrosine-protein kinase Src | 2.7.10.2 | 0.447 | |
| 3gts | D3M | DdmC | / | 0.447 | |
| 3kjs | NAP | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.447 | |
| 3lz6 | A0D | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.447 | |
| 4cvm | ANP | UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase | / | 0.447 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.447 | |
| 1g0n | NDP | Tetrahydroxynaphthalene reductase | 1.1.1.252 | 0.446 | |
| 1jtu | LYB | Thymidylate synthase | / | 0.446 | |
| 1qjf | ACS | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 1swn | BTN | Streptavidin | / | 0.446 | |
| 2chx | 090 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.446 | |
| 2p5y | NAD | UDP-glucose 4-epimerase | / | 0.446 | |
| 2w9h | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 3eku | CY9 | Actin-5C | / | 0.446 | |
| 3mpj | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.446 | |
| 4dpy | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.446 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.446 | |
| 4rrk | A3T | Probable threonine--tRNA ligase 2 | 6.1.1.3 | 0.446 | |
| 1o2g | 696 | Prothrombin | 3.4.21.5 | 0.445 | |
| 1v35 | NAI | Enoyl-ACP reductase | / | 0.445 | |
| 3gyt | DL4 | Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily | / | 0.445 | |
| 4cf6 | CBD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.445 | |
| 4g2y | NI5 | cGMP-specific 3',5'-cyclic phosphodiesterase | / | 0.445 | |
| 4wso | NAD | Probable nicotinate-nucleotide adenylyltransferase | / | 0.445 | |
| 5emh | NAP | Iridoid synthase | 1.3.1.99 | 0.445 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.444 | |
| 2r5n | TPP | Transketolase 1 | / | 0.444 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 3gvh | NAD | Malate dehydrogenase | / | 0.444 | |
| 3ivc | FG4 | Pantothenate synthetase | 6.3.2.1 | 0.444 | |
| 1amo | FAD | NADPH--cytochrome P450 reductase | / | 0.443 | |
| 1hdc | CBO | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.443 | |
| 1i5a | ACP | Chemotaxis protein CheA | 2.7.13.3 | 0.443 | |
| 1jnr | FAD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.443 | |
| 1kt3 | RTL | Retinol-binding protein 4 | / | 0.443 | |
| 1lf2 | R37 | Plasmepsin-2 | 3.4.23.39 | 0.443 | |
| 1rx8 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 1yvf | PH7 | Polyprotein | / | 0.443 | |
| 1zdw | FLV | Prenyltransferase | / | 0.443 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 3rdo | BTN | Streptavidin | / | 0.443 | |
| 4g2j | 0WF | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 1gj4 | 132 | Prothrombin | 3.4.21.5 | 0.442 | |
| 1mrq | STR | Aldo-keto reductase family 1 member C1 | / | 0.442 | |
| 1upc | TPP | N(2)-(2-carboxyethyl)arginine synthase | / | 0.442 | |
| 1y2b | DEE | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.442 | |
| 2a1h | GBN | Branched-chain-amino-acid aminotransferase, mitochondrial | 2.6.1.42 | 0.442 | |
| 2oci | TYC | Valacyclovir hydrolase | 3.1 | 0.442 | |
| 2w3b | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 3rl4 | 5GP | Metallophosphoesterase MPPED2 | 3.1 | 0.442 | |
| 3ujl | A8S | Abscisic acid receptor PYL2 | / | 0.442 | |
| 4mih | FAD | Pyranose 2-oxidase | 1.1.3.10 | 0.442 | |
| 4wdb | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.442 | |
| 5hes | 032 | Mitogen-activated protein kinase kinase kinase 20 | 2.7.11.25 | 0.442 | |
| 5pah | LDP | Phenylalanine-4-hydroxylase | 1.14.16.1 | 0.442 | |
| 1ai9 | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.441 | |
| 2ouu | 35G | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.441 | |
| 2xlu | NA7 | Putative flavin-containing monooxygenase | / | 0.441 | |
| 3e8x | NAP | BH1520 protein | / | 0.441 | |
| 3g45 | 988 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.441 | |
| 3l9l | L9L | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.441 | |
| 3qlr | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 4j03 | FVS | Bifunctional epoxide hydrolase 2 | 3.1.3.76 | 0.441 | |
| 4l1x | NAP | Aldo-keto reductase family 1 member C2 | / | 0.441 | |
| 5jy1 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.441 | |
| 1f4g | TP4 | Thymidylate synthase | / | 0.440 | |
| 1kt4 | RTL | Retinol-binding protein 4 | / | 0.440 | |
| 1wsv | THH | Aminomethyltransferase, mitochondrial | / | 0.440 | |
| 1z6t | ADP | Apoptotic protease-activating factor 1 | / | 0.440 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 2zhw | 12U | Prothrombin | 3.4.21.5 | 0.440 | |
| 3pvc | FAD | tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC | / | 0.440 | |
| 3uic | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.440 | |
| 4ocp | ADP | N-acetylhexosamine 1-kinase | 2.7.1.162 | 0.440 | |
| 4rnw | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.440 |