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 |
|---|---|---|---|
| 2zhq | 27U | Prothrombin | 3.4.21.5 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2zhq | 27U | Prothrombin | 3.4.21.5 | 1.000 | |
| 3hat | GLY_VAL_ARG_RNG | Prothrombin | 3.4.21.5 | 0.753 | |
| 2zgb | 21U | Prothrombin | 3.4.21.5 | 0.748 | |
| 2zgx | 29U | Prothrombin | 3.4.21.5 | 0.740 | |
| 2zhf | 49U | Prothrombin | 3.4.21.5 | 0.733 | |
| 3eq0 | 2TS | Prothrombin | 3.4.21.5 | 0.723 | |
| 2zhe | 13U | Prothrombin | 3.4.21.5 | 0.709 | |
| 4bah | MEL | Prothrombin | 3.4.21.5 | 0.709 | |
| 2znk | 31U | Prothrombin | 3.4.21.5 | 0.708 | |
| 2zdv | 37U | Prothrombin | 3.4.21.5 | 0.706 | |
| 2zff | 53U | Prothrombin | 3.4.21.5 | 0.704 | |
| 3biu | 10U | Prothrombin | 3.4.21.5 | 0.704 | |
| 2r2m | I50 | Prothrombin | 3.4.21.5 | 0.691 | |
| 4bao | MVF | Prothrombin | 3.4.21.5 | 0.688 | |
| 2zfr | 46U | Prothrombin | 3.4.21.5 | 0.679 | |
| 3qto | 10P | Prothrombin | 3.4.21.5 | 0.679 | |
| 1ypm | RA4 | Prothrombin | 3.4.21.5 | 0.676 | |
| 3dux | 64U | Prothrombin | 3.4.21.5 | 0.676 | |
| 2bdy | UNB | Prothrombin | 3.4.21.5 | 0.674 | |
| 3p17 | 99P | Prothrombin | 3.4.21.5 | 0.669 | |
| 1d3d | BZT | Prothrombin | 3.4.21.5 | 0.668 | |
| 2pks | G44 | Prothrombin | 3.4.21.5 | 0.666 | |
| 3qtv | 06P | Prothrombin | 3.4.21.5 | 0.664 | |
| 2zg0 | 50U | Prothrombin | 3.4.21.5 | 0.659 | |
| 1ghv | 120 | Prothrombin | 3.4.21.5 | 0.657 | |
| 2jh5 | 895 | Prothrombin | 3.4.21.5 | 0.645 | |
| 2zda | 32U | Prothrombin | 3.4.21.5 | 0.643 | |
| 2zi2 | 24U | Prothrombin | 3.4.21.5 | 0.640 | |
| 2anm | CDO | Prothrombin | 3.4.21.5 | 0.637 | |
| 2zhw | 12U | Prothrombin | 3.4.21.5 | 0.637 | |
| 1sb1 | 165 | Prothrombin | 3.4.21.5 | 0.634 | |
| 2zfp | 19U | Prothrombin | 3.4.21.5 | 0.634 | |
| 3qwc | 98P | Prothrombin | 3.4.21.5 | 0.630 | |
| 4bak | M67 | Prothrombin | 3.4.21.5 | 0.630 | |
| 2v3o | I26 | Prothrombin | 3.4.21.5 | 0.628 | |
| 4ax9 | N5N | Prothrombin | 3.4.21.5 | 0.627 | |
| 1nm6 | L86 | Prothrombin | 3.4.21.5 | 0.626 | |
| 2zf0 | 51U | Prothrombin | 3.4.21.5 | 0.624 | |
| 1d3p | BT3 | Prothrombin | 3.4.21.5 | 0.621 | |
| 2cf8 | ESH | Prothrombin | 3.4.21.5 | 0.620 | |
| 2v3h | I25 | Prothrombin | 3.4.21.5 | 0.620 | |
| 2uuk | 897 | Prothrombin | 3.4.21.5 | 0.617 | |
| 4bam | MM9 | Prothrombin | 3.4.21.5 | 0.617 | |
| 2zfq | 45U | Prothrombin | 3.4.21.5 | 0.613 | |
| 3c1k | T15 | Prothrombin | 3.4.21.5 | 0.612 | |
| 1jwt | BLI | Prothrombin | 3.4.21.5 | 0.610 | |
| 3c27 | DKK | Prothrombin | 3.4.21.5 | 0.610 | |
| 1gj5 | 130 | Prothrombin | 3.4.21.5 | 0.609 | |
| 4ayy | 9MX | Prothrombin | 3.4.21.5 | 0.604 | |
| 1bcu | PRL | Prothrombin | 3.4.21.5 | 0.602 | |
| 1ypk | CCR | Prothrombin | 3.4.21.5 | 0.601 | |
| 7kme | ACE_0BN_CHG_PRR | Prothrombin | 3.4.21.5 | 0.601 | |
| 1ype | UIP | Prothrombin | 3.4.21.5 | 0.599 | |
| 1o2g | 696 | Prothrombin | 3.4.21.5 | 0.598 | |
| 1t4u | 81A | Prothrombin | 3.4.21.5 | 0.594 | |
| 3biv | 11U | Prothrombin | 3.4.21.5 | 0.594 | |
| 3utu | 1TS | Prothrombin | 3.4.21.5 | 0.594 | |
| 1ypl | RA8 | Prothrombin | 3.4.21.5 | 0.593 | |
| 1zgi | 382 | Prothrombin | 3.4.21.5 | 0.593 | |
| 4n3l | 2FN | Prothrombin | 3.4.21.5 | 0.591 | |
| 1ta6 | 177 | Prothrombin | 3.4.21.5 | 0.589 | |
| 1z71 | L17 | Prothrombin | 3.4.21.5 | 0.587 | |
| 2bvs | 2CE | Prothrombin | 3.4.21.5 | 0.585 | |
| 1k21 | IGN | Prothrombin | 3.4.21.5 | 0.584 | |
| 2jh6 | 894 | Prothrombin | 3.4.21.5 | 0.583 | |
| 4ban | M6S | Prothrombin | 3.4.21.5 | 0.581 | |
| 1mue | CDD | Prothrombin | 3.4.21.5 | 0.580 | |
| 1c4y | IH3 | Prothrombin | 3.4.21.5 | 0.578 | |
| 1uma | IN2 | Prothrombin | 3.4.21.5 | 0.577 | |
| 2uuj | 896 | Prothrombin | 3.4.21.5 | 0.576 | |
| 4lxb | 7R9 | Prothrombin | 3.4.21.5 | 0.576 | |
| 1ae8 | AZL | Prothrombin | 3.4.21.5 | 0.574 | |
| 1d6w | 00R | Prothrombin | 3.4.21.5 | 0.574 | |
| 1oyt | FSN | Prothrombin | 3.4.21.5 | 0.574 | |
| 1t4v | 14A | Prothrombin | 3.4.21.5 | 0.574 | |
| 3dhk | 23U | Prothrombin | 3.4.21.5 | 0.573 | |
| 1mu6 | CDA | Prothrombin | 3.4.21.5 | 0.568 | |
| 1o5g | CR9 | Prothrombin | 3.4.21.5 | 0.566 | |
| 1zgv | 501 | Prothrombin | 3.4.21.5 | 0.565 | |
| 1a4w | QWE | Prothrombin | 3.4.21.5 | 0.564 | |
| 1afe | ALZ | Prothrombin | 3.4.21.5 | 0.563 | |
| 2cf9 | 348 | Prothrombin | 3.4.21.5 | 0.560 | |
| 4baq | M4Z | Prothrombin | 3.4.21.5 | 0.559 | |
| 1zrb | 062 | Prothrombin | 3.4.21.5 | 0.557 | |
| 1c4v | IH2 | Prothrombin | 3.4.21.5 | 0.556 | |
| 1nzq | 162 | Prothrombin | 3.4.21.5 | 0.554 | |
| 1vzq | SHY | Prothrombin | 3.4.21.5 | 0.553 | |
| 2ziq | 26U | Prothrombin | 3.4.21.5 | 0.552 | |
| 4az2 | 9MU | Prothrombin | 3.4.21.5 | 0.552 | |
| 4e7r | 0NW | Prothrombin | 3.4.21.5 | 0.545 | |
| 2bxt | C2D | Prothrombin | 3.4.21.5 | 0.541 | |
| 4rn6 | 15U | Prothrombin | 3.4.21.5 | 0.540 | |
| 3f68 | 91U | Prothrombin | 3.4.21.5 | 0.529 | |
| 1w7g | MIU | Prothrombin | 3.4.21.5 | 0.526 | |
| 1ny2 | ARG_PRO_PRO_GLY | Prothrombin | 3.4.21.5 | 0.524 | |
| 1c1u | BAI | Prothrombin | 3.4.21.5 | 0.519 | |
| 1mu8 | CDB | Prothrombin | 3.4.21.5 | 0.514 | |
| 1o0d | 163 | Prothrombin | 3.4.21.5 | 0.498 | |
| 1ypj | UIB | Prothrombin | 3.4.21.5 | 0.497 | |
| 4ayv | 9MQ | Prothrombin | 3.4.21.5 | 0.496 | |
| 3qdz | PRO_ALA_PRO_ARG | Prothrombin | 3.4.21.5 | 0.492 | |
| 3egk | M18 | Prothrombin | 3.4.21.5 | 0.490 | |
| 1c5n | ESI | Prothrombin | 3.4.21.5 | 0.489 | |
| 1gj4 | 132 | Prothrombin | 3.4.21.5 | 0.484 | |
| 1uvs | I11 | Prothrombin | 3.4.21.5 | 0.484 | |
| 1kts | C24 | Prothrombin | 3.4.21.5 | 0.480 | |
| 4loy | 6XS | Prothrombin | 3.4.21.5 | 0.466 | |
| 1sa5 | BMV | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.461 | |
| 4bby | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.456 | |
| 4btt | VYR | Coagulation factor X | 3.4.21.6 | 0.456 | |
| 1ta2 | 176 | Prothrombin | 3.4.21.5 | 0.454 | |
| 2whq | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.454 | |
| 1qoq | IGP | Tryptophan synthase alpha chain | / | 0.451 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.447 | |
| 2hxz | H7J | Cathepsin S | 3.4.22.27 | 0.447 | |
| 3q7f | ED2 | Uncharacterized protein | / | 0.447 | |
| 1fml | RTL | Retinol dehydratase | / | 0.446 | |
| 1nl4 | HFP | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.446 | |
| 3e30 | ED4 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.446 | |
| 4rlh | 0WE | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.446 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.445 | |
| 4x7z | ZM3 | Mycinamicin III 3''-O-methyltransferase | 2.1.1.237 | 0.444 | |
| 1j9z | FAD | NADPH--cytochrome P450 reductase | / | 0.443 | |
| 1ni4 | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.443 | |
| 1ni4 | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.443 | |
| 2ign | FAD | Pyranose 2-oxidase | / | 0.443 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial | 1.2.4.4 | 0.443 | |
| 2j9f | THV | 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial | 1.2.4.4 | 0.443 | |
| 4b1j | A1R | Poly(ADP-ribose) glycohydrolase | 3.2.1.143 | 0.443 | |
| 3zw9 | NAD | Peroxisomal bifunctional enzyme | 1.1.1.35 | 0.442 | |
| 4fam | 0SZ | Aldo-keto reductase family 1 member C3 | / | 0.442 | |
| 1o9b | NAI | Quinate/shikimate dehydrogenase | / | 0.440 | |
| 1q0r | AKT | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.440 | |
| 2i65 | NAD | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 | 3.2.2.6 | 0.440 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.440 |