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 |
|---|---|---|---|
| 3dux | 64U | Prothrombin | 3.4.21.5 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3dux | 64U | Prothrombin | 3.4.21.5 | 1.000 | |
| 3eq0 | 2TS | Prothrombin | 3.4.21.5 | 0.849 | |
| 2zgx | 29U | Prothrombin | 3.4.21.5 | 0.833 | |
| 2zgb | 21U | Prothrombin | 3.4.21.5 | 0.825 | |
| 2zf0 | 51U | Prothrombin | 3.4.21.5 | 0.815 | |
| 2zc9 | 22U | Prothrombin | 3.4.21.5 | 0.808 | |
| 2zhe | 13U | Prothrombin | 3.4.21.5 | 0.782 | |
| 4bam | MM9 | Prothrombin | 3.4.21.5 | 0.781 | |
| 2zdv | 37U | Prothrombin | 3.4.21.5 | 0.778 | |
| 2zhf | 49U | Prothrombin | 3.4.21.5 | 0.778 | |
| 4bak | M67 | Prothrombin | 3.4.21.5 | 0.761 | |
| 2zff | 53U | Prothrombin | 3.4.21.5 | 0.759 | |
| 3biu | 10U | Prothrombin | 3.4.21.5 | 0.757 | |
| 3hat | GLY_VAL_ARG_RNG | Prothrombin | 3.4.21.5 | 0.757 | |
| 2zfr | 46U | Prothrombin | 3.4.21.5 | 0.750 | |
| 2zfp | 19U | Prothrombin | 3.4.21.5 | 0.743 | |
| 2znk | 31U | Prothrombin | 3.4.21.5 | 0.742 | |
| 2zda | 32U | Prothrombin | 3.4.21.5 | 0.741 | |
| 2zhq | 27U | Prothrombin | 3.4.21.5 | 0.733 | |
| 4ban | M6S | Prothrombin | 3.4.21.5 | 0.717 | |
| 2zi2 | 24U | Prothrombin | 3.4.21.5 | 0.714 | |
| 2zg0 | 50U | Prothrombin | 3.4.21.5 | 0.713 | |
| 1zrb | 062 | Prothrombin | 3.4.21.5 | 0.703 | |
| 1afe | ALZ | Prothrombin | 3.4.21.5 | 0.700 | |
| 1t4v | 14A | Prothrombin | 3.4.21.5 | 0.698 | |
| 4baq | M4Z | Prothrombin | 3.4.21.5 | 0.694 | |
| 1mue | CDD | Prothrombin | 3.4.21.5 | 0.690 | |
| 1ypg | UIR | Prothrombin | 3.4.21.5 | 0.689 | |
| 7kme | ACE_0BN_CHG_PRR | Prothrombin | 3.4.21.5 | 0.683 | |
| 4bao | MVF | Prothrombin | 3.4.21.5 | 0.682 | |
| 2v3o | I26 | Prothrombin | 3.4.21.5 | 0.679 | |
| 1ta6 | 177 | Prothrombin | 3.4.21.5 | 0.676 | |
| 1ae8 | AZL | Prothrombin | 3.4.21.5 | 0.675 | |
| 1d6w | 00R | Prothrombin | 3.4.21.5 | 0.674 | |
| 1d3d | BZT | Prothrombin | 3.4.21.5 | 0.669 | |
| 1ype | UIP | Prothrombin | 3.4.21.5 | 0.669 | |
| 4bah | MEL | Prothrombin | 3.4.21.5 | 0.669 | |
| 2r2m | I50 | Prothrombin | 3.4.21.5 | 0.665 | |
| 3dhk | 23U | Prothrombin | 3.4.21.5 | 0.665 | |
| 1t4u | 81A | Prothrombin | 3.4.21.5 | 0.663 | |
| 1d4p | BPP | Prothrombin | 3.4.21.5 | 0.662 | |
| 2anm | CDO | Prothrombin | 3.4.21.5 | 0.662 | |
| 1mu6 | CDA | Prothrombin | 3.4.21.5 | 0.658 | |
| 1zgv | 501 | Prothrombin | 3.4.21.5 | 0.657 | |
| 1c4u | IH1 | Prothrombin | 3.4.21.5 | 0.655 | |
| 1k21 | IGN | Prothrombin | 3.4.21.5 | 0.654 | |
| 4n3l | 2FN | Prothrombin | 3.4.21.5 | 0.649 | |
| 1z71 | L17 | Prothrombin | 3.4.21.5 | 0.647 | |
| 2zhw | 12U | Prothrombin | 3.4.21.5 | 0.646 | |
| 2jh5 | 895 | Prothrombin | 3.4.21.5 | 0.645 | |
| 2uuk | 897 | Prothrombin | 3.4.21.5 | 0.645 | |
| 1ypl | RA8 | Prothrombin | 3.4.21.5 | 0.640 | |
| 1vzq | SHY | Prothrombin | 3.4.21.5 | 0.639 | |
| 1sb1 | 165 | Prothrombin | 3.4.21.5 | 0.638 | |
| 2pks | G44 | Prothrombin | 3.4.21.5 | 0.637 | |
| 1nzq | 162 | Prothrombin | 3.4.21.5 | 0.636 | |
| 3qto | 10P | Prothrombin | 3.4.21.5 | 0.633 | |
| 2jh6 | 894 | Prothrombin | 3.4.21.5 | 0.632 | |
| 2zfq | 45U | Prothrombin | 3.4.21.5 | 0.625 | |
| 3c1k | T15 | Prothrombin | 3.4.21.5 | 0.624 | |
| 1ypj | UIB | Prothrombin | 3.4.21.5 | 0.623 | |
| 3biv | 11U | Prothrombin | 3.4.21.5 | 0.623 | |
| 1xm1 | GAH | Prothrombin | 3.4.21.5 | 0.620 | |
| 2uuj | 896 | Prothrombin | 3.4.21.5 | 0.615 | |
| 3p17 | 99P | Prothrombin | 3.4.21.5 | 0.614 | |
| 1ypk | CCR | Prothrombin | 3.4.21.5 | 0.613 | |
| 3c27 | DKK | Prothrombin | 3.4.21.5 | 0.613 | |
| 1jwt | BLI | Prothrombin | 3.4.21.5 | 0.612 | |
| 4ayy | 9MX | Prothrombin | 3.4.21.5 | 0.612 | |
| 1d9i | 00P | Prothrombin | 3.4.21.5 | 0.610 | |
| 1a4w | QWE | Prothrombin | 3.4.21.5 | 0.609 | |
| 4ax9 | N5N | Prothrombin | 3.4.21.5 | 0.609 | |
| 1c4y | IH3 | Prothrombin | 3.4.21.5 | 0.607 | |
| 2cf9 | 348 | Prothrombin | 3.4.21.5 | 0.605 | |
| 1k22 | MEL | Prothrombin | 3.4.21.5 | 0.603 | |
| 1oyt | FSN | Prothrombin | 3.4.21.5 | 0.603 | |
| 2bdy | UNB | Prothrombin | 3.4.21.5 | 0.603 | |
| 4lxb | 7R9 | Prothrombin | 3.4.21.5 | 0.602 | |
| 2cf8 | ESH | Prothrombin | 3.4.21.5 | 0.600 | |
| 1zgi | 382 | Prothrombin | 3.4.21.5 | 0.598 | |
| 2bvs | 2CE | Prothrombin | 3.4.21.5 | 0.598 | |
| 1ypm | RA4 | Prothrombin | 3.4.21.5 | 0.596 | |
| 1d3p | BT3 | Prothrombin | 3.4.21.5 | 0.585 | |
| 4rn6 | 15U | Prothrombin | 3.4.21.5 | 0.580 | |
| 2gde | SN3 | Prothrombin | 3.4.21.5 | 0.579 | |
| 3qwc | 98P | Prothrombin | 3.4.21.5 | 0.579 | |
| 2jh0 | 701 | Prothrombin | 3.4.21.5 | 0.573 | |
| 3utu | 1TS | Prothrombin | 3.4.21.5 | 0.570 | |
| 2v3h | I25 | Prothrombin | 3.4.21.5 | 0.569 | |
| 2cn0 | F25 | Prothrombin | 3.4.21.5 | 0.565 | |
| 1nm6 | L86 | Prothrombin | 3.4.21.5 | 0.563 | |
| 2bxt | C2D | Prothrombin | 3.4.21.5 | 0.562 | |
| 4az2 | 9MU | Prothrombin | 3.4.21.5 | 0.562 | |
| 3qtv | 06P | Prothrombin | 3.4.21.5 | 0.552 | |
| 3f68 | 91U | Prothrombin | 3.4.21.5 | 0.537 | |
| 1w7g | MIU | Prothrombin | 3.4.21.5 | 0.530 | |
| 5cmx | 0G6 | Prothrombin | 3.4.21.5 | 0.516 | |
| 2ziq | 26U | Prothrombin | 3.4.21.5 | 0.515 | |
| 1c4v | IH2 | Prothrombin | 3.4.21.5 | 0.511 | |
| 4ayv | 9MQ | Prothrombin | 3.4.21.5 | 0.510 | |
| 1ny2 | ARG_PRO_PRO_GLY | Prothrombin | 3.4.21.5 | 0.508 | |
| 1o0d | 163 | Prothrombin | 3.4.21.5 | 0.504 | |
| 1riw | OSC | Prothrombin | 3.4.21.5 | 0.501 | |
| 1uma | IN2 | Prothrombin | 3.4.21.5 | 0.501 | |
| 2ign | FAD | Pyranose 2-oxidase | / | 0.495 | |
| 1ta2 | 176 | Prothrombin | 3.4.21.5 | 0.487 | |
| 4bby | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.487 | |
| 4loy | 6XS | Prothrombin | 3.4.21.5 | 0.485 | |
| 4f1l | 0RY | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.484 | |
| 3oqf | S51 | Renin | 3.4.23.15 | 0.482 | |
| 4bca | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.476 | |
| 1mu8 | CDB | Prothrombin | 3.4.21.5 | 0.474 | |
| 3ig6 | 438 | Urokinase-type plasminogen activator | 3.4.21.73 | 0.473 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.473 | |
| 3qdz | PRO_ALA_PRO_ARG | Prothrombin | 3.4.21.5 | 0.471 | |
| 4b1j | A1R | Poly(ADP-ribose) glycohydrolase | 3.2.1.143 | 0.469 | |
| 4gv4 | MEJ | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.468 | |
| 3qgf | 46F | Genome polyprotein | 2.7.7.48 | 0.467 | |
| 1kvr | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.464 | |
| 2wu4 | HBP | Acetylcholinesterase | 3.1.1.7 | 0.464 | |
| 3ozd | 4CT | S-methyl-5'-thioadenosine phosphorylase | / | 0.464 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.463 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.461 | |
| 1ghv | 120 | Prothrombin | 3.4.21.5 | 0.460 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.460 | |
| 1nsg | RAD | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.458 | |
| 1nsg | RAD | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.458 | |
| 1s20 | NAD | 2,3-diketo-L-gulonate reductase | 1.1.1.130 | 0.458 | |
| 2fap | RAD | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.456 | |
| 2fap | RAD | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.456 | |
| 3jqp | A2P | Ferredoxin--NADP reductase, apicoplast | / | 0.456 | |
| 5c6c | CMP | cGMP-dependent protein kinase 2 | 2.7.11.12 | 0.456 | |
| 5doz | NDP | JamJ | / | 0.456 | |
| 2b8l | 5HA | Beta-secretase 1 | 3.4.23.46 | 0.455 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.455 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.454 | |
| 1sa5 | BMV | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.452 | |
| 3eks | CY9 | Actin-5C | / | 0.452 | |
| 4xgu | ADP | Putative pachytene checkpoint protein 2 | / | 0.451 | |
| 1cul | FOK | Adenylate cyclase type 2 | / | 0.450 | |
| 1cul | FOK | Adenylate cyclase type 5 | / | 0.450 | |
| 3bg7 | FAD | Pyranose 2-oxidase | / | 0.450 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.450 | |
| 1j9z | FAD | NADPH--cytochrome P450 reductase | / | 0.449 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.449 | |
| 3ha5 | SFG | Hydroxymycolate synthase MmaA4 | 2.1.1 | 0.449 | |
| 3own | 3OW | Renin | 3.4.23.15 | 0.449 | |
| 4phl | PIL | Phosphodiesterase | / | 0.449 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.448 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.448 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.448 | |
| 2hiz | LIJ | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 3k4n | FAD | Pyranose 2-oxidase | / | 0.448 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.447 | |
| 1ib0 | NAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.447 | |
| 1upw | 444 | Oxysterols receptor LXR-beta | / | 0.447 | |
| 4c4o | NAD | SADH | / | 0.447 | |
| 1dxq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.446 | |
| 2wf3 | ZY3 | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 4a31 | 2CB | Glycylpeptide N-tetradecanoyltransferase | / | 0.446 | |
| 2hq9 | FAD | Mll6688 protein | / | 0.445 | |
| 2j3j | HC4 | NADPH-dependent oxidoreductase 2-alkenal reductase | 1.3.1.74 | 0.445 | |
| 3eku | CY9 | Actin-5C | / | 0.445 | |
| 4d03 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.445 | |
| 4uth | FMN | Xenobiotic reductase | / | 0.445 | |
| 1e3e | NAI | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.444 | |
| 1gg5 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.444 | |
| 2a2x | NA9 | Prothrombin | 3.4.21.5 | 0.444 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.444 | |
| 2gyw | OBI | Acetylcholinesterase | 3.1.1.7 | 0.444 | |
| 3v76 | FDA | Uncharacterized protein | / | 0.444 | |
| 4btt | VYR | Coagulation factor X | 3.4.21.6 | 0.444 | |
| 4idg | NAD | Putative UDP-glucose 4-epimerase | / | 0.444 | |
| 2j83 | BAT | Ulilysin | 3.4.24 | 0.443 | |
| 3fbu | COA | Acetyltransferase, GNAT family | / | 0.443 | |
| 4hfr | 14M | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.443 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.442 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 3c15 | FOK | Adenylate cyclase type 2 | / | 0.442 | |
| 3c15 | FOK | Adenylate cyclase type 5 | / | 0.442 | |
| 5dp2 | NAP | CurF | / | 0.442 | |
| 5ig2 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.442 | |
| 1ju2 | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.441 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 4bc7 | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.441 | |
| 4zu4 | 4TG | WxcM-like protein | / | 0.441 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 1xs7 | MMI | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 2iqg | F2I | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 2jbs | FMN | p-hydroxyphenylacetate 3-hydroxylase, oxygenase component | / | 0.440 | |
| 2q1t | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.440 | |
| 2xuh | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 2z3u | CRR | Cytochrome P450 | / | 0.440 | |
| 3nu0 | 3TU | Dihydrofolate reductase | 1.5.1.3 | 0.440 | |
| 4k8s | 1QT | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4ynt | FDA | Glucose oxidase, putative | / | 0.440 |