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 |
|---|---|---|---|
| 4bak | M67 | Prothrombin | 3.4.21.5 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4bak | M67 | Prothrombin | 3.4.21.5 | 1.000 | |
| 4bam | MM9 | Prothrombin | 3.4.21.5 | 0.812 | |
| 7kme | ACE_0BN_CHG_PRR | Prothrombin | 3.4.21.5 | 0.787 | |
| 4ban | M6S | Prothrombin | 3.4.21.5 | 0.786 | |
| 4baq | M4Z | Prothrombin | 3.4.21.5 | 0.784 | |
| 2zgb | 21U | Prothrombin | 3.4.21.5 | 0.774 | |
| 2zgx | 29U | Prothrombin | 3.4.21.5 | 0.759 | |
| 3eq0 | 2TS | Prothrombin | 3.4.21.5 | 0.759 | |
| 2znk | 31U | Prothrombin | 3.4.21.5 | 0.756 | |
| 3dux | 64U | Prothrombin | 3.4.21.5 | 0.743 | |
| 4bao | MVF | Prothrombin | 3.4.21.5 | 0.726 | |
| 2zf0 | 51U | Prothrombin | 3.4.21.5 | 0.725 | |
| 2zhe | 13U | Prothrombin | 3.4.21.5 | 0.724 | |
| 2zdv | 37U | Prothrombin | 3.4.21.5 | 0.707 | |
| 2zc9 | 22U | Prothrombin | 3.4.21.5 | 0.698 | |
| 2zda | 32U | Prothrombin | 3.4.21.5 | 0.696 | |
| 2zff | 53U | Prothrombin | 3.4.21.5 | 0.689 | |
| 3biu | 10U | Prothrombin | 3.4.21.5 | 0.684 | |
| 2zfr | 46U | Prothrombin | 3.4.21.5 | 0.678 | |
| 1afe | ALZ | Prothrombin | 3.4.21.5 | 0.676 | |
| 4bah | MEL | Prothrombin | 3.4.21.5 | 0.676 | |
| 1zrb | 062 | Prothrombin | 3.4.21.5 | 0.675 | |
| 3hat | GLY_VAL_ARG_RNG | Prothrombin | 3.4.21.5 | 0.672 | |
| 1mue | CDD | Prothrombin | 3.4.21.5 | 0.660 | |
| 2zfq | 45U | Prothrombin | 3.4.21.5 | 0.655 | |
| 2zhq | 27U | Prothrombin | 3.4.21.5 | 0.655 | |
| 2zhf | 49U | Prothrombin | 3.4.21.5 | 0.650 | |
| 1d6w | 00R | Prothrombin | 3.4.21.5 | 0.648 | |
| 1ta6 | 177 | Prothrombin | 3.4.21.5 | 0.648 | |
| 1t4v | 14A | Prothrombin | 3.4.21.5 | 0.644 | |
| 1k21 | IGN | Prothrombin | 3.4.21.5 | 0.638 | |
| 2r2m | I50 | Prothrombin | 3.4.21.5 | 0.637 | |
| 1z71 | L17 | Prothrombin | 3.4.21.5 | 0.634 | |
| 1t4u | 81A | Prothrombin | 3.4.21.5 | 0.631 | |
| 1ae8 | AZL | Prothrombin | 3.4.21.5 | 0.630 | |
| 2zg0 | 50U | Prothrombin | 3.4.21.5 | 0.628 | |
| 2v3o | I26 | Prothrombin | 3.4.21.5 | 0.627 | |
| 3qto | 10P | Prothrombin | 3.4.21.5 | 0.624 | |
| 1c4u | IH1 | Prothrombin | 3.4.21.5 | 0.623 | |
| 1k22 | MEL | Prothrombin | 3.4.21.5 | 0.623 | |
| 2zfp | 19U | Prothrombin | 3.4.21.5 | 0.623 | |
| 2anm | CDO | Prothrombin | 3.4.21.5 | 0.621 | |
| 1ypl | RA8 | Prothrombin | 3.4.21.5 | 0.620 | |
| 1zgv | 501 | Prothrombin | 3.4.21.5 | 0.620 | |
| 1d3d | BZT | Prothrombin | 3.4.21.5 | 0.617 | |
| 1d4p | BPP | Prothrombin | 3.4.21.5 | 0.615 | |
| 1vzq | SHY | Prothrombin | 3.4.21.5 | 0.615 | |
| 2bxt | C2D | Prothrombin | 3.4.21.5 | 0.614 | |
| 2pks | G44 | Prothrombin | 3.4.21.5 | 0.612 | |
| 1ypj | UIB | Prothrombin | 3.4.21.5 | 0.611 | |
| 1mu6 | CDA | Prothrombin | 3.4.21.5 | 0.604 | |
| 1sb1 | 165 | Prothrombin | 3.4.21.5 | 0.599 | |
| 1jwt | BLI | Prothrombin | 3.4.21.5 | 0.595 | |
| 3p17 | 99P | Prothrombin | 3.4.21.5 | 0.595 | |
| 4n3l | 2FN | Prothrombin | 3.4.21.5 | 0.595 | |
| 1nzq | 162 | Prothrombin | 3.4.21.5 | 0.594 | |
| 4e7r | 0NW | Prothrombin | 3.4.21.5 | 0.591 | |
| 1zgi | 382 | Prothrombin | 3.4.21.5 | 0.589 | |
| 2zhw | 12U | Prothrombin | 3.4.21.5 | 0.586 | |
| 4ax9 | N5N | Prothrombin | 3.4.21.5 | 0.585 | |
| 2uuk | 897 | Prothrombin | 3.4.21.5 | 0.584 | |
| 3c1k | T15 | Prothrombin | 3.4.21.5 | 0.584 | |
| 2uuj | 896 | Prothrombin | 3.4.21.5 | 0.582 | |
| 1xm1 | GAH | Prothrombin | 3.4.21.5 | 0.578 | |
| 2jh5 | 895 | Prothrombin | 3.4.21.5 | 0.576 | |
| 4ayy | 9MX | Prothrombin | 3.4.21.5 | 0.576 | |
| 2jh6 | 894 | Prothrombin | 3.4.21.5 | 0.574 | |
| 1a4w | QWE | Prothrombin | 3.4.21.5 | 0.572 | |
| 3c27 | DKK | Prothrombin | 3.4.21.5 | 0.571 | |
| 1ypk | CCR | Prothrombin | 3.4.21.5 | 0.570 | |
| 4lxb | 7R9 | Prothrombin | 3.4.21.5 | 0.563 | |
| 1c4y | IH3 | Prothrombin | 3.4.21.5 | 0.562 | |
| 1d9i | 00P | Prothrombin | 3.4.21.5 | 0.562 | |
| 1ypm | RA4 | Prothrombin | 3.4.21.5 | 0.562 | |
| 1bcu | PRL | Prothrombin | 3.4.21.5 | 0.561 | |
| 1oyt | FSN | Prothrombin | 3.4.21.5 | 0.561 | |
| 4az2 | 9MU | Prothrombin | 3.4.21.5 | 0.560 | |
| 3biv | 11U | Prothrombin | 3.4.21.5 | 0.555 | |
| 2bdy | UNB | Prothrombin | 3.4.21.5 | 0.553 | |
| 1d3p | BT3 | Prothrombin | 3.4.21.5 | 0.538 | |
| 1nm6 | L86 | Prothrombin | 3.4.21.5 | 0.538 | |
| 2gde | SN3 | Prothrombin | 3.4.21.5 | 0.538 | |
| 1w7g | MIU | Prothrombin | 3.4.21.5 | 0.535 | |
| 1ghv | 120 | Prothrombin | 3.4.21.5 | 0.530 | |
| 3utu | 1TS | Prothrombin | 3.4.21.5 | 0.527 | |
| 2cf8 | ESH | Prothrombin | 3.4.21.5 | 0.524 | |
| 2v3h | I25 | Prothrombin | 3.4.21.5 | 0.524 | |
| 1gj5 | 130 | Prothrombin | 3.4.21.5 | 0.520 | |
| 1c1u | BAI | Prothrombin | 3.4.21.5 | 0.516 | |
| 3qtv | 06P | Prothrombin | 3.4.21.5 | 0.516 | |
| 5cmx | 0G6 | Prothrombin | 3.4.21.5 | 0.516 | |
| 1o2g | 696 | Prothrombin | 3.4.21.5 | 0.511 | |
| 1o5g | CR9 | Prothrombin | 3.4.21.5 | 0.510 | |
| 1uma | IN2 | Prothrombin | 3.4.21.5 | 0.510 | |
| 2ziq | 26U | Prothrombin | 3.4.21.5 | 0.510 | |
| 3qwc | 98P | Prothrombin | 3.4.21.5 | 0.502 | |
| 1riw | OSC | Prothrombin | 3.4.21.5 | 0.501 | |
| 1o0d | 163 | Prothrombin | 3.4.21.5 | 0.484 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.469 | |
| 1ny2 | ARG_PRO_PRO_GLY | Prothrombin | 3.4.21.5 | 0.468 | |
| 1c4v | IH2 | Prothrombin | 3.4.21.5 | 0.464 | |
| 1fml | RTL | Retinol dehydratase | / | 0.461 | |
| 3f68 | 91U | Prothrombin | 3.4.21.5 | 0.457 | |
| 2pg0 | FAD | Acyl-CoA dehydrogenase | / | 0.456 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.455 | |
| 1mu8 | CDB | Prothrombin | 3.4.21.5 | 0.454 | |
| 3k4n | FAD | Pyranose 2-oxidase | / | 0.454 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.452 | |
| 2wu4 | HBP | Acetylcholinesterase | 3.1.1.7 | 0.451 | |
| 2znn | S44 | Peroxisome proliferator-activated receptor alpha | / | 0.450 | |
| 3uxv | GUN | NADPH-dependent 7-cyano-7-deazaguanine reductase | / | 0.450 | |
| 2pci | SAH | Diphthine synthase | / | 0.449 | |
| 2uxo | TAC | HTH-type transcriptional regulator TtgR | / | 0.449 | |
| 2wf1 | ZY1 | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 3ada | NAD | Subunit alpha of sarocosine oxidase | / | 0.448 | |
| 3ou2 | SAH | SAM-dependent methyltransferase | / | 0.448 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.447 | |
| 3nmp | PYV | Abscisic acid receptor PYL2 | / | 0.447 | |
| 2hxz | H7J | Cathepsin S | 3.4.22.27 | 0.446 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.446 | |
| 4h6p | FMN | Chromate reductase | / | 0.446 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.445 | |
| 3ozd | 4CT | S-methyl-5'-thioadenosine phosphorylase | / | 0.445 | |
| 2cv2 | GSU | Glutamate--tRNA ligase | 6.1.1.17 | 0.444 | |
| 3ens | ENS | Coagulation factor X | 3.4.21.6 | 0.444 | |
| 4e32 | DWN | Methyltransferase | / | 0.444 | |
| 1c5n | ESI | Prothrombin | 3.4.21.5 | 0.443 | |
| 2ek2 | SAH | Diphthine synthase | / | 0.443 | |
| 2p2x | SAH | Diphthine synthase | / | 0.443 | |
| 2yk2 | YJW | Heat shock protein HSP 90-alpha | / | 0.443 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 4arb | C57 | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 2egs | SAH | Diphthine synthase | / | 0.442 | |
| 2yk2 | YJX | Heat shock protein HSP 90-alpha | / | 0.442 | |
| 4rlh | 0WE | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.442 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.441 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.440 | |
| 1s20 | NAD | 2,3-diketo-L-gulonate reductase | 1.1.1.130 | 0.440 | |
| 1xds | DRA | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.440 | |
| 2dv3 | SAH | Diphthine synthase | / | 0.440 | |
| 2ign | FAD | Pyranose 2-oxidase | / | 0.440 | |
| 2wf3 | ZY3 | Beta-secretase 1 | 3.4.23.46 | 0.440 |