sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
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
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 3biu | 10U | Prothrombin | 3.4.21.5 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3biu | 10U | Prothrombin | 3.4.21.5 | 1.000 | |
| 2zgx | 29U | Prothrombin | 3.4.21.5 | 0.810 | |
| 2znk | 31U | Prothrombin | 3.4.21.5 | 0.796 | |
| 2zhf | 49U | Prothrombin | 3.4.21.5 | 0.794 | |
| 2zfr | 46U | Prothrombin | 3.4.21.5 | 0.791 | |
| 2zi2 | 24U | Prothrombin | 3.4.21.5 | 0.783 | |
| 2zda | 32U | Prothrombin | 3.4.21.5 | 0.781 | |
| 2zg0 | 50U | Prothrombin | 3.4.21.5 | 0.780 | |
| 2zdv | 37U | Prothrombin | 3.4.21.5 | 0.779 | |
| 3hat | GLY_VAL_ARG_RNG | Prothrombin | 3.4.21.5 | 0.774 | |
| 2zhe | 13U | Prothrombin | 3.4.21.5 | 0.761 | |
| 3dux | 64U | Prothrombin | 3.4.21.5 | 0.747 | |
| 2zc9 | 22U | Prothrombin | 3.4.21.5 | 0.740 | |
| 2zff | 53U | Prothrombin | 3.4.21.5 | 0.738 | |
| 2zhq | 27U | Prothrombin | 3.4.21.5 | 0.736 | |
| 3eq0 | 2TS | Prothrombin | 3.4.21.5 | 0.733 | |
| 4bam | MM9 | Prothrombin | 3.4.21.5 | 0.722 | |
| 2zgb | 21U | Prothrombin | 3.4.21.5 | 0.717 | |
| 4ax9 | N5N | Prothrombin | 3.4.21.5 | 0.708 | |
| 4bak | M67 | Prothrombin | 3.4.21.5 | 0.700 | |
| 1ypg | UIR | Prothrombin | 3.4.21.5 | 0.699 | |
| 2zfp | 19U | Prothrombin | 3.4.21.5 | 0.698 | |
| 1ype | UIP | Prothrombin | 3.4.21.5 | 0.690 | |
| 7kme | ACE_0BN_CHG_PRR | Prothrombin | 3.4.21.5 | 0.684 | |
| 1c4u | IH1 | Prothrombin | 3.4.21.5 | 0.672 | |
| 1d4p | BPP | Prothrombin | 3.4.21.5 | 0.671 | |
| 2zfq | 45U | Prothrombin | 3.4.21.5 | 0.671 | |
| 2zhw | 12U | Prothrombin | 3.4.21.5 | 0.671 | |
| 3biv | 11U | Prothrombin | 3.4.21.5 | 0.670 | |
| 2v3o | I26 | Prothrombin | 3.4.21.5 | 0.665 | |
| 1afe | ALZ | Prothrombin | 3.4.21.5 | 0.664 | |
| 1zrb | 062 | Prothrombin | 3.4.21.5 | 0.659 | |
| 2r2m | I50 | Prothrombin | 3.4.21.5 | 0.658 | |
| 2zf0 | 51U | Prothrombin | 3.4.21.5 | 0.657 | |
| 1mue | CDD | Prothrombin | 3.4.21.5 | 0.654 | |
| 3p17 | 99P | Prothrombin | 3.4.21.5 | 0.653 | |
| 4ban | M6S | Prothrombin | 3.4.21.5 | 0.652 | |
| 1ypj | UIB | Prothrombin | 3.4.21.5 | 0.650 | |
| 1d3d | BZT | Prothrombin | 3.4.21.5 | 0.649 | |
| 1ae8 | AZL | Prothrombin | 3.4.21.5 | 0.648 | |
| 1d6w | 00R | Prothrombin | 3.4.21.5 | 0.646 | |
| 2jh5 | 895 | Prothrombin | 3.4.21.5 | 0.645 | |
| 1k21 | IGN | Prothrombin | 3.4.21.5 | 0.644 | |
| 2bdy | UNB | Prothrombin | 3.4.21.5 | 0.644 | |
| 3dhk | 23U | Prothrombin | 3.4.21.5 | 0.642 | |
| 4bao | MVF | Prothrombin | 3.4.21.5 | 0.642 | |
| 1sb1 | 165 | Prothrombin | 3.4.21.5 | 0.641 | |
| 2anm | CDO | Prothrombin | 3.4.21.5 | 0.641 | |
| 3qwc | 98P | Prothrombin | 3.4.21.5 | 0.639 | |
| 1xm1 | GAH | Prothrombin | 3.4.21.5 | 0.631 | |
| 1t4v | 14A | Prothrombin | 3.4.21.5 | 0.629 | |
| 3qto | 10P | Prothrombin | 3.4.21.5 | 0.629 | |
| 1ypl | RA8 | Prothrombin | 3.4.21.5 | 0.625 | |
| 4baq | M4Z | Prothrombin | 3.4.21.5 | 0.625 | |
| 1jwt | BLI | Prothrombin | 3.4.21.5 | 0.624 | |
| 2jh6 | 894 | Prothrombin | 3.4.21.5 | 0.624 | |
| 4ayy | 9MX | Prothrombin | 3.4.21.5 | 0.621 | |
| 2uuk | 897 | Prothrombin | 3.4.21.5 | 0.620 | |
| 1vzq | SHY | Prothrombin | 3.4.21.5 | 0.617 | |
| 3c1k | T15 | Prothrombin | 3.4.21.5 | 0.617 | |
| 1mu6 | CDA | Prothrombin | 3.4.21.5 | 0.616 | |
| 1ta6 | 177 | Prothrombin | 3.4.21.5 | 0.616 | |
| 2jh0 | 701 | Prothrombin | 3.4.21.5 | 0.616 | |
| 1d9i | 00P | Prothrombin | 3.4.21.5 | 0.615 | |
| 1oyt | FSN | Prothrombin | 3.4.21.5 | 0.615 | |
| 1ypm | RA4 | Prothrombin | 3.4.21.5 | 0.614 | |
| 2pks | G44 | Prothrombin | 3.4.21.5 | 0.614 | |
| 4n3l | 2FN | Prothrombin | 3.4.21.5 | 0.614 | |
| 2bvs | 2CE | Prothrombin | 3.4.21.5 | 0.611 | |
| 1t4u | 81A | Prothrombin | 3.4.21.5 | 0.610 | |
| 2ziq | 26U | Prothrombin | 3.4.21.5 | 0.608 | |
| 1c4y | IH3 | Prothrombin | 3.4.21.5 | 0.606 | |
| 1nm6 | L86 | Prothrombin | 3.4.21.5 | 0.603 | |
| 3c27 | DKK | Prothrombin | 3.4.21.5 | 0.602 | |
| 1ypk | CCR | Prothrombin | 3.4.21.5 | 0.601 | |
| 1z71 | L17 | Prothrombin | 3.4.21.5 | 0.601 | |
| 4bah | MEL | Prothrombin | 3.4.21.5 | 0.600 | |
| 1d3p | BT3 | Prothrombin | 3.4.21.5 | 0.597 | |
| 1zgv | 501 | Prothrombin | 3.4.21.5 | 0.595 | |
| 4lxb | 7R9 | Prothrombin | 3.4.21.5 | 0.592 | |
| 2cf9 | 348 | Prothrombin | 3.4.21.5 | 0.588 | |
| 1k22 | MEL | Prothrombin | 3.4.21.5 | 0.585 | |
| 2uuj | 896 | Prothrombin | 3.4.21.5 | 0.580 | |
| 1nzq | 162 | Prothrombin | 3.4.21.5 | 0.579 | |
| 4e7r | 0NW | Prothrombin | 3.4.21.5 | 0.578 | |
| 4rn6 | 15U | Prothrombin | 3.4.21.5 | 0.573 | |
| 3utu | 1TS | Prothrombin | 3.4.21.5 | 0.572 | |
| 1zgi | 382 | Prothrombin | 3.4.21.5 | 0.570 | |
| 2cf8 | ESH | Prothrombin | 3.4.21.5 | 0.567 | |
| 4az2 | 9MU | Prothrombin | 3.4.21.5 | 0.566 | |
| 2v3h | I25 | Prothrombin | 3.4.21.5 | 0.565 | |
| 2gde | SN3 | Prothrombin | 3.4.21.5 | 0.564 | |
| 1a4w | QWE | Prothrombin | 3.4.21.5 | 0.563 | |
| 2cn0 | F25 | Prothrombin | 3.4.21.5 | 0.558 | |
| 3qtv | 06P | Prothrombin | 3.4.21.5 | 0.550 | |
| 4ayv | 9MQ | Prothrombin | 3.4.21.5 | 0.549 | |
| 1riw | OSC | Prothrombin | 3.4.21.5 | 0.537 | |
| 5cmx | 0G6 | Prothrombin | 3.4.21.5 | 0.534 | |
| 1w7g | MIU | Prothrombin | 3.4.21.5 | 0.531 | |
| 3egk | M18 | Prothrombin | 3.4.21.5 | 0.531 | |
| 1o0d | 163 | Prothrombin | 3.4.21.5 | 0.528 | |
| 2bxt | C2D | Prothrombin | 3.4.21.5 | 0.522 | |
| 3f68 | 91U | Prothrombin | 3.4.21.5 | 0.522 | |
| 1c4v | IH2 | Prothrombin | 3.4.21.5 | 0.517 | |
| 3qdz | PRO_ALA_PRO_ARG | Prothrombin | 3.4.21.5 | 0.507 | |
| 1ny2 | ARG_PRO_PRO_GLY | Prothrombin | 3.4.21.5 | 0.505 | |
| 1uvs | I11 | Prothrombin | 3.4.21.5 | 0.502 | |
| 4hfp | 15U | Prothrombin | 3.4.21.5 | 0.500 | |
| 1kts | C24 | Prothrombin | 3.4.21.5 | 0.493 | |
| 1mu8 | CDB | Prothrombin | 3.4.21.5 | 0.492 | |
| 1ghv | 120 | Prothrombin | 3.4.21.5 | 0.491 | |
| 4loy | 6XS | Prothrombin | 3.4.21.5 | 0.490 | |
| 2j83 | BAT | Ulilysin | 3.4.24 | 0.482 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.477 | |
| 1uma | IN2 | Prothrombin | 3.4.21.5 | 0.471 | |
| 1bcu | PRL | Prothrombin | 3.4.21.5 | 0.469 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.464 | |
| 1cul | FOK | Adenylate cyclase type 2 | / | 0.462 | |
| 1cul | FOK | Adenylate cyclase type 5 | / | 0.462 | |
| 1ju2 | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.462 | |
| 1kvr | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.462 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.462 | |
| 3qgf | 46F | Genome polyprotein | 2.7.7.48 | 0.462 | |
| 2c4f | GIL | Coagulation factor VII | 3.4.21.21 | 0.461 | |
| 3vil | SA0 | Beta-glucosidase | / | 0.461 | |
| 3ig6 | 438 | Urokinase-type plasminogen activator | 3.4.21.73 | 0.460 | |
| 3k1w | BFX | Renin | 3.4.23.15 | 0.459 | |
| 3own | 3OW | Renin | 3.4.23.15 | 0.459 | |
| 4gv4 | MEJ | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.459 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.458 | |
| 2z3u | CRR | Cytochrome P450 | / | 0.458 | |
| 3oqf | S51 | Renin | 3.4.23.15 | 0.458 | |
| 4ey6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.458 | |
| 5c6c | CMP | cGMP-dependent protein kinase 2 | 2.7.11.12 | 0.457 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.456 | |
| 4a80 | 2AN | Major pollen allergen Bet v 1-A | / | 0.456 | |
| 4b1j | A1R | Poly(ADP-ribose) glycohydrolase | 3.2.1.143 | 0.456 | |
| 2xvi | FAD | Putative flavin-containing monooxygenase | / | 0.455 | |
| 4lxj | LAN | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.455 | |
| 2g22 | 6IG | Renin | 3.4.23.15 | 0.454 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.454 | |
| 4arb | C57 | Acetylcholinesterase | 3.1.1.7 | 0.454 | |
| 4h6p | FMN | Chromate reductase | / | 0.453 | |
| 2a2x | NA9 | Prothrombin | 3.4.21.5 | 0.452 | |
| 3bg7 | FAD | Pyranose 2-oxidase | / | 0.452 | |
| 1gj4 | 132 | Prothrombin | 3.4.21.5 | 0.451 | |
| 1mvs | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 1oc1 | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 1wn3 | HXC | Phenylacetic acid degradation protein PaaI | / | 0.449 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.449 | |
| 3wtk | TH4 | Acetylcholine-binding protein | / | 0.449 | |
| 2fzw | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.448 | |
| 4gv0 | 8ME | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.448 | |
| 1mvt | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 3rdq | DTB | Streptavidin | / | 0.447 | |
| 4cf6 | CBD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.447 | |
| 5eb5 | FAD | (R)-mandelonitrile lyase 1 | 4.1.2.10 | 0.447 | |
| 1sa5 | BMV | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.446 | |
| 2fze | APR | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.446 | |
| 3v76 | FDA | Uncharacterized protein | / | 0.446 | |
| 4bc7 | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.446 | |
| 4mlp | 2CX | Cryptochrome-2 | / | 0.446 | |
| 5a88 | ADP | Riboflavin biosynthesis protein RibF | 2.7.1.26 | 0.446 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 3ozd | 4CT | S-methyl-5'-thioadenosine phosphorylase | / | 0.445 | |
| 4e2d | FMN | Dehydrogenase | / | 0.445 | |
| 4rlh | 0WE | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.445 | |
| 4xsv | C5P | Ethanolamine-phosphate cytidylyltransferase | 2.7.7.14 | 0.445 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.444 | |
| 1q0r | AKT | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.444 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.444 | |
| 2iqg | F2I | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 4f1l | 0RY | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.444 | |
| 4nv0 | MG7 | 7-methylguanosine phosphate-specific 5'-nucleotidase | / | 0.444 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.444 | |
| 1jtv | TES | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.443 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.443 | |
| 2wf3 | ZY3 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 3q7f | ED2 | Uncharacterized protein | / | 0.443 | |
| 4bby | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.443 | |
| 4bge | PYW | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.443 | |
| 2pbw | DOQ | Glutamate receptor ionotropic, kainate 1 | / | 0.442 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 4kby | C2E | Stimulator of interferon genes protein | / | 0.442 | |
| 4r81 | FMN | Predicted NADH dehydrogenase | / | 0.442 | |
| 4ara | C56 | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 4d03 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.441 | |
| 4f32 | N32 | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | / | 0.441 | |
| 4gxs | 0YS | Glutamate receptor 2 | / | 0.441 | |
| 5dp2 | NAP | CurF | / | 0.441 | |
| 5irn | ADP | Nucleotide binding oligomerization domain containing 2 | / | 0.441 | |
| 1cju | FOK | Adenylate cyclase type 2 | / | 0.440 | |
| 1cju | FOK | Adenylate cyclase type 5 | / | 0.440 | |
| 1fml | RTL | Retinol dehydratase | / | 0.440 | |
| 1r2j | FAD | FkbI | / | 0.440 | |
| 2wu4 | HBP | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 3fcj | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.440 | |
| 3vyf | VYF | Renin | 3.4.23.15 | 0.440 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.440 | |
| 4xgu | ADP | Putative pachytene checkpoint protein 2 | / | 0.440 |