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 |
|---|---|---|---|
| 3qtv | 06P | Prothrombin | 3.4.21.5 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3qtv | 06P | Prothrombin | 3.4.21.5 | 1.000 | |
| 3p17 | 99P | Prothrombin | 3.4.21.5 | 0.834 | |
| 3qto | 10P | Prothrombin | 3.4.21.5 | 0.823 | |
| 2zhq | 27U | Prothrombin | 3.4.21.5 | 0.758 | |
| 4bao | MVF | Prothrombin | 3.4.21.5 | 0.753 | |
| 2zff | 53U | Prothrombin | 3.4.21.5 | 0.689 | |
| 4bah | MEL | Prothrombin | 3.4.21.5 | 0.684 | |
| 2zhw | 12U | Prothrombin | 3.4.21.5 | 0.677 | |
| 3qwc | 98P | Prothrombin | 3.4.21.5 | 0.672 | |
| 2zgx | 29U | Prothrombin | 3.4.21.5 | 0.666 | |
| 2zdv | 37U | Prothrombin | 3.4.21.5 | 0.654 | |
| 2zhf | 49U | Prothrombin | 3.4.21.5 | 0.652 | |
| 2zgb | 21U | Prothrombin | 3.4.21.5 | 0.651 | |
| 3c27 | DKK | Prothrombin | 3.4.21.5 | 0.650 | |
| 1nzq | 162 | Prothrombin | 3.4.21.5 | 0.645 | |
| 1d3d | BZT | Prothrombin | 3.4.21.5 | 0.641 | |
| 1ypm | RA4 | Prothrombin | 3.4.21.5 | 0.640 | |
| 2bdy | UNB | Prothrombin | 3.4.21.5 | 0.637 | |
| 1ghv | 120 | Prothrombin | 3.4.21.5 | 0.635 | |
| 2zfp | 19U | Prothrombin | 3.4.21.5 | 0.635 | |
| 3hat | GLY_VAL_ARG_RNG | Prothrombin | 3.4.21.5 | 0.635 | |
| 3utu | 1TS | Prothrombin | 3.4.21.5 | 0.635 | |
| 1o2g | 696 | Prothrombin | 3.4.21.5 | 0.634 | |
| 3eq0 | 2TS | Prothrombin | 3.4.21.5 | 0.629 | |
| 2zhe | 13U | Prothrombin | 3.4.21.5 | 0.615 | |
| 2pks | G44 | Prothrombin | 3.4.21.5 | 0.613 | |
| 2v3h | I25 | Prothrombin | 3.4.21.5 | 0.612 | |
| 1sb1 | 165 | Prothrombin | 3.4.21.5 | 0.611 | |
| 5cmx | 0G6 | Prothrombin | 3.4.21.5 | 0.610 | |
| 1nm6 | L86 | Prothrombin | 3.4.21.5 | 0.609 | |
| 2znk | 31U | Prothrombin | 3.4.21.5 | 0.607 | |
| 1jwt | BLI | Prothrombin | 3.4.21.5 | 0.605 | |
| 1ypj | UIB | Prothrombin | 3.4.21.5 | 0.603 | |
| 1gj5 | 130 | Prothrombin | 3.4.21.5 | 0.602 | |
| 1k22 | MEL | Prothrombin | 3.4.21.5 | 0.599 | |
| 1zgv | 501 | Prothrombin | 3.4.21.5 | 0.593 | |
| 3biu | 10U | Prothrombin | 3.4.21.5 | 0.593 | |
| 3c1k | T15 | Prothrombin | 3.4.21.5 | 0.591 | |
| 2r2m | I50 | Prothrombin | 3.4.21.5 | 0.590 | |
| 1d3p | BT3 | Prothrombin | 3.4.21.5 | 0.589 | |
| 1a4w | QWE | Prothrombin | 3.4.21.5 | 0.588 | |
| 2zg0 | 50U | Prothrombin | 3.4.21.5 | 0.588 | |
| 4ban | M6S | Prothrombin | 3.4.21.5 | 0.586 | |
| 1t4u | 81A | Prothrombin | 3.4.21.5 | 0.585 | |
| 1ypk | CCR | Prothrombin | 3.4.21.5 | 0.583 | |
| 1t4v | 14A | Prothrombin | 3.4.21.5 | 0.582 | |
| 3dux | 64U | Prothrombin | 3.4.21.5 | 0.582 | |
| 4ayy | 9MX | Prothrombin | 3.4.21.5 | 0.581 | |
| 1ta6 | 177 | Prothrombin | 3.4.21.5 | 0.579 | |
| 4bak | M67 | Prothrombin | 3.4.21.5 | 0.578 | |
| 4n3l | 2FN | Prothrombin | 3.4.21.5 | 0.577 | |
| 1bcu | PRL | Prothrombin | 3.4.21.5 | 0.576 | |
| 4ax9 | N5N | Prothrombin | 3.4.21.5 | 0.574 | |
| 4baq | M4Z | Prothrombin | 3.4.21.5 | 0.574 | |
| 1afe | ALZ | Prothrombin | 3.4.21.5 | 0.571 | |
| 2zfq | 45U | Prothrombin | 3.4.21.5 | 0.570 | |
| 2zf0 | 51U | Prothrombin | 3.4.21.5 | 0.567 | |
| 4bam | MM9 | Prothrombin | 3.4.21.5 | 0.566 | |
| 1d6w | 00R | Prothrombin | 3.4.21.5 | 0.564 | |
| 4az2 | 9MU | Prothrombin | 3.4.21.5 | 0.564 | |
| 2bxt | C2D | Prothrombin | 3.4.21.5 | 0.562 | |
| 1z71 | L17 | Prothrombin | 3.4.21.5 | 0.559 | |
| 1ae8 | AZL | Prothrombin | 3.4.21.5 | 0.558 | |
| 3qdz | PRO_ALA_PRO_ARG | Prothrombin | 3.4.21.5 | 0.558 | |
| 2uuk | 897 | Prothrombin | 3.4.21.5 | 0.557 | |
| 1ypl | RA8 | Prothrombin | 3.4.21.5 | 0.555 | |
| 1zgi | 382 | Prothrombin | 3.4.21.5 | 0.553 | |
| 2bvs | 2CE | Prothrombin | 3.4.21.5 | 0.553 | |
| 4lxb | 7R9 | Prothrombin | 3.4.21.5 | 0.551 | |
| 7kme | ACE_0BN_CHG_PRR | Prothrombin | 3.4.21.5 | 0.544 | |
| 4e7r | 0NW | Prothrombin | 3.4.21.5 | 0.543 | |
| 1mu6 | CDA | Prothrombin | 3.4.21.5 | 0.542 | |
| 1mue | CDD | Prothrombin | 3.4.21.5 | 0.541 | |
| 1uma | IN2 | Prothrombin | 3.4.21.5 | 0.541 | |
| 1vzq | SHY | Prothrombin | 3.4.21.5 | 0.540 | |
| 2uuj | 896 | Prothrombin | 3.4.21.5 | 0.538 | |
| 1w7g | MIU | Prothrombin | 3.4.21.5 | 0.537 | |
| 1zrb | 062 | Prothrombin | 3.4.21.5 | 0.537 | |
| 1c4y | IH3 | Prothrombin | 3.4.21.5 | 0.535 | |
| 2jh6 | 894 | Prothrombin | 3.4.21.5 | 0.535 | |
| 1c4v | IH2 | Prothrombin | 3.4.21.5 | 0.534 | |
| 1c1u | BAI | Prothrombin | 3.4.21.5 | 0.531 | |
| 1ny2 | ARG_PRO_PRO_GLY | Prothrombin | 3.4.21.5 | 0.518 | |
| 3biv | 11U | Prothrombin | 3.4.21.5 | 0.518 | |
| 1d4p | BPP | Prothrombin | 3.4.21.5 | 0.513 | |
| 1mu8 | CDB | Prothrombin | 3.4.21.5 | 0.512 | |
| 1k21 | IGN | Prothrombin | 3.4.21.5 | 0.511 | |
| 2ziq | 26U | Prothrombin | 3.4.21.5 | 0.509 | |
| 4rn6 | 15U | Prothrombin | 3.4.21.5 | 0.507 | |
| 1riw | OSC | Prothrombin | 3.4.21.5 | 0.506 | |
| 1o0d | 163 | Prothrombin | 3.4.21.5 | 0.500 | |
| 1gj4 | 132 | Prothrombin | 3.4.21.5 | 0.495 | |
| 4loy | 6XS | Prothrombin | 3.4.21.5 | 0.490 | |
| 1c1w | BAH | Prothrombin | 3.4.21.5 | 0.485 | |
| 3fp0 | FP0 | 15-O-acetyltransferase | / | 0.485 | |
| 3f68 | 91U | Prothrombin | 3.4.21.5 | 0.484 | |
| 1ni4 | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.474 | |
| 1ni4 | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.474 | |
| 4lxa | 1YS | Beta-secretase 1 | 3.4.23.46 | 0.471 | |
| 4bby | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.468 | |
| 1ta2 | 176 | Prothrombin | 3.4.21.5 | 0.467 | |
| 1u1g | BBB | Uridine phosphorylase | 2.4.2.3 | 0.466 | |
| 2cbr | A80 | Cellular retinoic acid-binding protein 1 | / | 0.465 | |
| 3hk1 | B64 | Fatty acid-binding protein, adipocyte | / | 0.465 | |
| 3uxv | GUN | NADPH-dependent 7-cyano-7-deazaguanine reductase | / | 0.465 | |
| 3dva | TPW | Pyruvate dehydrogenase E1 component subunit alpha | 1.2.4.1 | 0.463 | |
| 3dva | TPW | Pyruvate dehydrogenase E1 component subunit beta | 1.2.4.1 | 0.463 | |
| 3b6p | TMP | Three-prime repair exonuclease 1 | 3.1.11.2 | 0.461 | |
| 3lpj | Z75 | Beta-secretase 1 | 3.4.23.46 | 0.461 | |
| 3zc5 | W9Z | Hepatocyte growth factor receptor | 2.7.10.1 | 0.459 | |
| 3s2v | 3HU | Glutamate receptor ionotropic, kainate 1 | / | 0.457 | |
| 4b0c | C9H | 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase | 4.2.1.59 | 0.456 | |
| 4d89 | BXD | Beta-secretase 1 | 3.4.23.46 | 0.456 | |
| 4frk | DWD | Beta-secretase 1 | 3.4.23.46 | 0.456 | |
| 1tll | FMN | Nitric oxide synthase, brain | 1.14.13.39 | 0.455 | |
| 2wu4 | HBP | Acetylcholinesterase | 3.1.1.7 | 0.455 | |
| 3eku | CY9 | Actin-5C | / | 0.454 | |
| 1knr | FAD | L-aspartate oxidase | 1.4.3.16 | 0.453 | |
| 2hp2 | KE4 | Glutamate-1-semialdehyde 2,1-aminomutase | 5.4.3.8 | 0.453 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.452 | |
| 3qvr | FAD | Glucose oxidase | 1.1.3.4 | 0.452 | |
| 1rkw | PNT | HTH-type transcriptional regulator QacR | / | 0.451 | |
| 2zz0 | FAD | Thioredoxin reductase 1, cytoplasmic | 1.8.1.9 | 0.451 | |
| 3tfu | PL8 | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase | 2.6.1.62 | 0.451 | |
| 3uxy | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.451 | |
| 3v76 | FDA | Uncharacterized protein | / | 0.451 | |
| 3zu2 | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.451 | |
| 4jtq | NAP | Aldo-keto reductase family 1 member C2 | / | 0.451 | |
| 1p0p | BCH | Cholinesterase | 3.1.1.8 | 0.450 | |
| 1toj | HCI | Aspartate aminotransferase | 2.6.1.1 | 0.450 | |
| 2ed3 | SAH | Diphthine synthase | / | 0.450 | |
| 3atz | FMN | Prostaglandin F2a synthase | / | 0.450 | |
| 3eks | CY9 | Actin-5C | / | 0.450 | |
| 3exf | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.450 | |
| 3exf | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.450 | |
| 4gv4 | MEJ | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.450 | |
| 1c3x | 8IG | Purine nucleoside phosphorylase | 2.4.2.1 | 0.449 | |
| 1dx6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.449 | |
| 1fml | RTL | Retinol dehydratase | / | 0.449 | |
| 1typ | FAD | Trypanothione reductase | 1.8.1.12 | 0.449 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.449 | |
| 2ohj | FMN | Type A flavoprotein FprA | 1 | 0.449 | |
| 4euf | NAD | Trans-2-enoyl-CoA reductase [NADH] | / | 0.449 | |
| 2v2z | ADP | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.448 | |
| 3eah | 327 | Nitric oxide synthase, endothelial | 1.14.13.39 | 0.448 | |
| 3ivc | FG4 | Pantothenate synthetase | 6.3.2.1 | 0.448 | |
| 4qai | FMN | NADPH dehydrogenase | / | 0.448 | |
| 4rvn | COA | Phenylacetate-coenzyme A ligase | / | 0.448 | |
| 4ure | 1PS | Cyclohexanol dehydrogenase | / | 0.448 | |
| 1c5n | ESI | Prothrombin | 3.4.21.5 | 0.447 | |
| 1d2h | SAH | Glycine N-methyltransferase | 2.1.1.20 | 0.447 | |
| 3cgt | BCD | Cyclomaltodextrin glucanotransferase | 2.4.1.19 | 0.447 | |
| 1j9z | FAD | NADPH--cytochrome P450 reductase | / | 0.446 | |
| 1pyd | TDP | Pyruvate decarboxylase isozyme 1 | / | 0.446 | |
| 2a2x | NA9 | Prothrombin | 3.4.21.5 | 0.446 | |
| 3hlw | CE3 | Beta-lactamase | / | 0.446 | |
| 3b8z | 294 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.445 | |
| 3fr5 | I4A | Fatty acid-binding protein, adipocyte | / | 0.445 | |
| 4a80 | 2AN | Major pollen allergen Bet v 1-A | / | 0.445 | |
| 4c73 | TLH | 3-oxoacyl-ACP synthase | / | 0.445 | |
| 4f32 | N32 | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | / | 0.445 | |
| 2f99 | AKV | Aklanonic acid methyl ester cyclase AcmA | 5.5.1.23 | 0.444 | |
| 2p9c | NAI | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.444 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.443 | |
| 2hxz | H7J | Cathepsin S | 3.4.22.27 | 0.443 | |
| 3ihz | FK5 | Peptidylprolyl isomerase | / | 0.443 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 4psb | GA3 | Cytokinin-specific binding protein | / | 0.443 | |
| 1fvp | FMA | Non-fluorescent flavoprotein | / | 0.442 | |
| 2o12 | FMN | Chorismate synthase | / | 0.442 | |
| 2rd6 | 78P | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.442 | |
| 4b1j | A1R | Poly(ADP-ribose) glycohydrolase | 3.2.1.143 | 0.442 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.442 | |
| 3ozd | 4CT | S-methyl-5'-thioadenosine phosphorylase | / | 0.441 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 1qoq | IGP | Tryptophan synthase alpha chain | / | 0.440 | |
| 1qrp | HH0 | Pepsin A-4 | 3.4.23.1 | 0.440 | |
| 2a0y | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.440 | |
| 2ggs | NDP | dTDP-4-dehydrorhamnose reductase | / | 0.440 | |
| 2jdt | I5S | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.440 | |
| 3rdq | DTB | Streptavidin | / | 0.440 | |
| 4frj | DWB | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4pzr | COA | Histone acetyltransferase p300 | / | 0.440 | |
| 4uug | PXG | Branched-chain amino acid aminotransferase, putative | / | 0.440 |