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 |
|---|---|---|---|
| 3qwc | 98P | Prothrombin | 3.4.21.5 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3qwc | 98P | Prothrombin | 3.4.21.5 | 1.000 | |
| 3c1k | T15 | Prothrombin | 3.4.21.5 | 0.708 | |
| 1oyt | FSN | Prothrombin | 3.4.21.5 | 0.705 | |
| 1ta6 | 177 | Prothrombin | 3.4.21.5 | 0.695 | |
| 4ax9 | N5N | Prothrombin | 3.4.21.5 | 0.695 | |
| 1ypl | RA8 | Prothrombin | 3.4.21.5 | 0.691 | |
| 1nm6 | L86 | Prothrombin | 3.4.21.5 | 0.688 | |
| 2zfq | 45U | Prothrombin | 3.4.21.5 | 0.678 | |
| 1z71 | L17 | Prothrombin | 3.4.21.5 | 0.677 | |
| 2zhw | 12U | Prothrombin | 3.4.21.5 | 0.674 | |
| 1mu6 | CDA | Prothrombin | 3.4.21.5 | 0.671 | |
| 2cn0 | F25 | Prothrombin | 3.4.21.5 | 0.669 | |
| 2cf8 | ESH | Prothrombin | 3.4.21.5 | 0.666 | |
| 1t4v | 14A | Prothrombin | 3.4.21.5 | 0.665 | |
| 2r2m | I50 | Prothrombin | 3.4.21.5 | 0.665 | |
| 1t4u | 81A | Prothrombin | 3.4.21.5 | 0.663 | |
| 1ypm | RA4 | Prothrombin | 3.4.21.5 | 0.658 | |
| 2zc9 | 22U | Prothrombin | 3.4.21.5 | 0.654 | |
| 1d3p | BT3 | Prothrombin | 3.4.21.5 | 0.652 | |
| 2zfr | 46U | Prothrombin | 3.4.21.5 | 0.652 | |
| 1d9i | 00P | Prothrombin | 3.4.21.5 | 0.649 | |
| 2zi2 | 24U | Prothrombin | 3.4.21.5 | 0.648 | |
| 2bdy | UNB | Prothrombin | 3.4.21.5 | 0.646 | |
| 2zhf | 49U | Prothrombin | 3.4.21.5 | 0.644 | |
| 2jh5 | 895 | Prothrombin | 3.4.21.5 | 0.643 | |
| 2anm | CDO | Prothrombin | 3.4.21.5 | 0.642 | |
| 2zda | 32U | Prothrombin | 3.4.21.5 | 0.640 | |
| 3p17 | 99P | Prothrombin | 3.4.21.5 | 0.637 | |
| 4ayy | 9MX | Prothrombin | 3.4.21.5 | 0.637 | |
| 4n3l | 2FN | Prothrombin | 3.4.21.5 | 0.635 | |
| 1xm1 | GAH | Prothrombin | 3.4.21.5 | 0.634 | |
| 1ypj | UIB | Prothrombin | 3.4.21.5 | 0.634 | |
| 2jh6 | 894 | Prothrombin | 3.4.21.5 | 0.631 | |
| 2cf9 | 348 | Prothrombin | 3.4.21.5 | 0.628 | |
| 1c4y | IH3 | Prothrombin | 3.4.21.5 | 0.624 | |
| 1d6w | 00R | Prothrombin | 3.4.21.5 | 0.624 | |
| 2v3h | I25 | Prothrombin | 3.4.21.5 | 0.617 | |
| 1nzq | 162 | Prothrombin | 3.4.21.5 | 0.616 | |
| 1zgi | 382 | Prothrombin | 3.4.21.5 | 0.614 | |
| 2zhq | 27U | Prothrombin | 3.4.21.5 | 0.614 | |
| 2jh0 | 701 | Prothrombin | 3.4.21.5 | 0.612 | |
| 3hat | GLY_VAL_ARG_RNG | Prothrombin | 3.4.21.5 | 0.611 | |
| 2gde | SN3 | Prothrombin | 3.4.21.5 | 0.610 | |
| 1zgv | 501 | Prothrombin | 3.4.21.5 | 0.607 | |
| 1ypk | CCR | Prothrombin | 3.4.21.5 | 0.605 | |
| 4lxb | 7R9 | Prothrombin | 3.4.21.5 | 0.599 | |
| 1d3d | BZT | Prothrombin | 3.4.21.5 | 0.598 | |
| 1zrb | 062 | Prothrombin | 3.4.21.5 | 0.598 | |
| 2uuk | 897 | Prothrombin | 3.4.21.5 | 0.598 | |
| 2zg0 | 50U | Prothrombin | 3.4.21.5 | 0.598 | |
| 1c4u | IH1 | Prothrombin | 3.4.21.5 | 0.596 | |
| 1sb1 | 165 | Prothrombin | 3.4.21.5 | 0.596 | |
| 1jwt | BLI | Prothrombin | 3.4.21.5 | 0.595 | |
| 2bvs | 2CE | Prothrombin | 3.4.21.5 | 0.592 | |
| 2zfp | 19U | Prothrombin | 3.4.21.5 | 0.590 | |
| 1a4w | QWE | Prothrombin | 3.4.21.5 | 0.589 | |
| 3qto | 10P | Prothrombin | 3.4.21.5 | 0.589 | |
| 4az2 | 9MU | Prothrombin | 3.4.21.5 | 0.588 | |
| 2v3o | I26 | Prothrombin | 3.4.21.5 | 0.587 | |
| 2zff | 53U | Prothrombin | 3.4.21.5 | 0.587 | |
| 1k22 | MEL | Prothrombin | 3.4.21.5 | 0.586 | |
| 1d4p | BPP | Prothrombin | 3.4.21.5 | 0.585 | |
| 1ypg | UIR | Prothrombin | 3.4.21.5 | 0.585 | |
| 1ype | UIP | Prothrombin | 3.4.21.5 | 0.581 | |
| 2zgx | 29U | Prothrombin | 3.4.21.5 | 0.581 | |
| 2zdv | 37U | Prothrombin | 3.4.21.5 | 0.580 | |
| 1mue | CDD | Prothrombin | 3.4.21.5 | 0.579 | |
| 2znk | 31U | Prothrombin | 3.4.21.5 | 0.578 | |
| 3biu | 10U | Prothrombin | 3.4.21.5 | 0.574 | |
| 3qtv | 06P | Prothrombin | 3.4.21.5 | 0.573 | |
| 3utu | 1TS | Prothrombin | 3.4.21.5 | 0.573 | |
| 2pks | G44 | Prothrombin | 3.4.21.5 | 0.572 | |
| 1ae8 | AZL | Prothrombin | 3.4.21.5 | 0.564 | |
| 4bah | MEL | Prothrombin | 3.4.21.5 | 0.564 | |
| 4ayv | 9MQ | Prothrombin | 3.4.21.5 | 0.562 | |
| 1mu8 | CDB | Prothrombin | 3.4.21.5 | 0.554 | |
| 2zhe | 13U | Prothrombin | 3.4.21.5 | 0.554 | |
| 1afe | ALZ | Prothrombin | 3.4.21.5 | 0.553 | |
| 3eq0 | 2TS | Prothrombin | 3.4.21.5 | 0.548 | |
| 1k21 | IGN | Prothrombin | 3.4.21.5 | 0.547 | |
| 4e7r | 0NW | Prothrombin | 3.4.21.5 | 0.547 | |
| 4bao | MVF | Prothrombin | 3.4.21.5 | 0.539 | |
| 1c4v | IH2 | Prothrombin | 3.4.21.5 | 0.537 | |
| 1vzq | SHY | Prothrombin | 3.4.21.5 | 0.535 | |
| 2zgb | 21U | Prothrombin | 3.4.21.5 | 0.535 | |
| 5cmx | 0G6 | Prothrombin | 3.4.21.5 | 0.533 | |
| 1riw | OSC | Prothrombin | 3.4.21.5 | 0.532 | |
| 2uuj | 896 | Prothrombin | 3.4.21.5 | 0.532 | |
| 1w7g | MIU | Prothrombin | 3.4.21.5 | 0.530 | |
| 2ziq | 26U | Prothrombin | 3.4.21.5 | 0.530 | |
| 4bam | MM9 | Prothrombin | 3.4.21.5 | 0.526 | |
| 3c27 | DKK | Prothrombin | 3.4.21.5 | 0.525 | |
| 3dux | 64U | Prothrombin | 3.4.21.5 | 0.525 | |
| 3qdz | PRO_ALA_PRO_ARG | Prothrombin | 3.4.21.5 | 0.518 | |
| 2a2x | NA9 | Prothrombin | 3.4.21.5 | 0.516 | |
| 2zf0 | 51U | Prothrombin | 3.4.21.5 | 0.513 | |
| 3biv | 11U | Prothrombin | 3.4.21.5 | 0.501 | |
| 2bxt | C2D | Prothrombin | 3.4.21.5 | 0.498 | |
| 7kme | ACE_0BN_CHG_PRR | Prothrombin | 3.4.21.5 | 0.492 | |
| 1uma | IN2 | Prothrombin | 3.4.21.5 | 0.488 | |
| 4baq | M4Z | Prothrombin | 3.4.21.5 | 0.487 | |
| 3dhk | 23U | Prothrombin | 3.4.21.5 | 0.486 | |
| 4hfp | 15U | Prothrombin | 3.4.21.5 | 0.484 | |
| 1ghv | 120 | Prothrombin | 3.4.21.5 | 0.479 | |
| 4ban | M6S | Prothrombin | 3.4.21.5 | 0.479 | |
| 4bak | M67 | Prothrombin | 3.4.21.5 | 0.477 | |
| 1ju2 | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.468 | |
| 2fap | RAD | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.468 | |
| 2fap | RAD | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.468 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.465 | |
| 1nsg | RAD | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.464 | |
| 1nsg | RAD | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.464 | |
| 1bcu | PRL | Prothrombin | 3.4.21.5 | 0.461 | |
| 3egk | M18 | Prothrombin | 3.4.21.5 | 0.460 | |
| 1gj4 | 132 | Prothrombin | 3.4.21.5 | 0.459 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.458 | |
| 1kts | C24 | Prothrombin | 3.4.21.5 | 0.455 | |
| 1uvs | I11 | Prothrombin | 3.4.21.5 | 0.455 | |
| 1cf3 | FAD | Glucose oxidase | 1.1.3.4 | 0.454 | |
| 1o0d | 163 | Prothrombin | 3.4.21.5 | 0.454 | |
| 3ada | NAD | Subunit alpha of sarocosine oxidase | / | 0.452 | |
| 4acx | S8Z | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 1ny2 | ARG_PRO_PRO_GLY | Prothrombin | 3.4.21.5 | 0.450 | |
| 4b12 | C23 | Glycylpeptide N-tetradecanoyltransferase | / | 0.450 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.449 | |
| 4drj | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.448 | |
| 4drj | RAP | Peptidyl-prolyl cis-trans isomerase FKBP4 | 5.2.1.8 | 0.448 | |
| 3ig6 | 438 | Urokinase-type plasminogen activator | 3.4.21.73 | 0.447 | |
| 4brd | ANP | Ectonucleoside triphosphate diphosphohydrolase I | / | 0.447 | |
| 1c7o | PPG | Hemolysin | / | 0.446 | |
| 2g1y | 5IG | Renin | 3.4.23.15 | 0.444 | |
| 3oqf | S51 | Renin | 3.4.23.15 | 0.444 | |
| 3ppk | FNI | Serine/threonine-protein kinase B-raf | 2.7.11.1 | 0.444 | |
| 4azy | 7F3 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 4bby | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.442 | |
| 5cho | FAD | Flavin reductase | / | 0.442 | |
| 2g20 | L1A | Renin | 3.4.23.15 | 0.441 | |
| 4dri | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.441 | |
| 4dri | RAP | Peptidyl-prolyl cis-trans isomerase FKBP5 | 5.2.1.8 | 0.441 | |
| 4kby | C2E | Stimulator of interferon genes protein | / | 0.441 | |
| 1q0r | AKT | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.440 | |
| 1u1g | BBB | Uridine phosphorylase | 2.4.2.3 | 0.440 | |
| 3cid | 318 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 3ozd | 4CT | S-methyl-5'-thioadenosine phosphorylase | / | 0.440 | |
| 3q43 | D66 | M1 family aminopeptidase | 3.4.11 | 0.440 | |
| 4bca | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.440 |