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 |
|---|---|---|---|
| 2uuj | 896 | Prothrombin | 3.4.21.5 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2uuj | 896 | Prothrombin | 3.4.21.5 | 1.000 | |
| 1xm1 | GAH | Prothrombin | 3.4.21.5 | 0.699 | |
| 2uuk | 897 | Prothrombin | 3.4.21.5 | 0.659 | |
| 1sb1 | 165 | Prothrombin | 3.4.21.5 | 0.657 | |
| 4n3l | 2FN | Prothrombin | 3.4.21.5 | 0.650 | |
| 1z71 | L17 | Prothrombin | 3.4.21.5 | 0.649 | |
| 1ta6 | 177 | Prothrombin | 3.4.21.5 | 0.643 | |
| 1zgi | 382 | Prothrombin | 3.4.21.5 | 0.642 | |
| 1ypm | RA4 | Prothrombin | 3.4.21.5 | 0.641 | |
| 1d9i | 00P | Prothrombin | 3.4.21.5 | 0.640 | |
| 2zda | 32U | Prothrombin | 3.4.21.5 | 0.636 | |
| 1d6w | 00R | Prothrombin | 3.4.21.5 | 0.635 | |
| 3c1k | T15 | Prothrombin | 3.4.21.5 | 0.634 | |
| 2bdy | UNB | Prothrombin | 3.4.21.5 | 0.630 | |
| 3eq0 | 2TS | Prothrombin | 3.4.21.5 | 0.630 | |
| 2pks | G44 | Prothrombin | 3.4.21.5 | 0.629 | |
| 2v3o | I26 | Prothrombin | 3.4.21.5 | 0.628 | |
| 2zf0 | 51U | Prothrombin | 3.4.21.5 | 0.627 | |
| 2zhf | 49U | Prothrombin | 3.4.21.5 | 0.626 | |
| 1mue | CDD | Prothrombin | 3.4.21.5 | 0.625 | |
| 2zgb | 21U | Prothrombin | 3.4.21.5 | 0.625 | |
| 2zhq | 27U | Prothrombin | 3.4.21.5 | 0.623 | |
| 1t4v | 14A | Prothrombin | 3.4.21.5 | 0.622 | |
| 2zfq | 45U | Prothrombin | 3.4.21.5 | 0.622 | |
| 2jh5 | 895 | Prothrombin | 3.4.21.5 | 0.620 | |
| 2zff | 53U | Prothrombin | 3.4.21.5 | 0.619 | |
| 3dux | 64U | Prothrombin | 3.4.21.5 | 0.617 | |
| 2v3h | I25 | Prothrombin | 3.4.21.5 | 0.616 | |
| 1ypg | UIR | Prothrombin | 3.4.21.5 | 0.614 | |
| 1k22 | MEL | Prothrombin | 3.4.21.5 | 0.613 | |
| 2zgx | 29U | Prothrombin | 3.4.21.5 | 0.613 | |
| 1d3d | BZT | Prothrombin | 3.4.21.5 | 0.612 | |
| 2zfr | 46U | Prothrombin | 3.4.21.5 | 0.612 | |
| 1mu6 | CDA | Prothrombin | 3.4.21.5 | 0.611 | |
| 1d3p | BT3 | Prothrombin | 3.4.21.5 | 0.608 | |
| 2zdv | 37U | Prothrombin | 3.4.21.5 | 0.608 | |
| 4bam | MM9 | Prothrombin | 3.4.21.5 | 0.608 | |
| 2jh0 | 701 | Prothrombin | 3.4.21.5 | 0.607 | |
| 4ax9 | N5N | Prothrombin | 3.4.21.5 | 0.607 | |
| 1afe | ALZ | Prothrombin | 3.4.21.5 | 0.606 | |
| 1ypl | RA8 | Prothrombin | 3.4.21.5 | 0.606 | |
| 2znk | 31U | Prothrombin | 3.4.21.5 | 0.606 | |
| 1nm6 | L86 | Prothrombin | 3.4.21.5 | 0.604 | |
| 2zi2 | 24U | Prothrombin | 3.4.21.5 | 0.602 | |
| 4bah | MEL | Prothrombin | 3.4.21.5 | 0.602 | |
| 4lxb | 7R9 | Prothrombin | 3.4.21.5 | 0.602 | |
| 1ae8 | AZL | Prothrombin | 3.4.21.5 | 0.601 | |
| 2zc9 | 22U | Prothrombin | 3.4.21.5 | 0.601 | |
| 2zg0 | 50U | Prothrombin | 3.4.21.5 | 0.601 | |
| 2zhw | 12U | Prothrombin | 3.4.21.5 | 0.601 | |
| 1ypk | CCR | Prothrombin | 3.4.21.5 | 0.599 | |
| 1zrb | 062 | Prothrombin | 3.4.21.5 | 0.598 | |
| 2cn0 | F25 | Prothrombin | 3.4.21.5 | 0.598 | |
| 4bak | M67 | Prothrombin | 3.4.21.5 | 0.597 | |
| 7kme | ACE_0BN_CHG_PRR | Prothrombin | 3.4.21.5 | 0.597 | |
| 4ayy | 9MX | Prothrombin | 3.4.21.5 | 0.596 | |
| 2jh6 | 894 | Prothrombin | 3.4.21.5 | 0.592 | |
| 2zfp | 19U | Prothrombin | 3.4.21.5 | 0.592 | |
| 3biu | 10U | Prothrombin | 3.4.21.5 | 0.590 | |
| 1c4y | IH3 | Prothrombin | 3.4.21.5 | 0.589 | |
| 2anm | CDO | Prothrombin | 3.4.21.5 | 0.587 | |
| 2cf8 | ESH | Prothrombin | 3.4.21.5 | 0.587 | |
| 1oyt | FSN | Prothrombin | 3.4.21.5 | 0.586 | |
| 2bxt | C2D | Prothrombin | 3.4.21.5 | 0.585 | |
| 3qwc | 98P | Prothrombin | 3.4.21.5 | 0.584 | |
| 1d4p | BPP | Prothrombin | 3.4.21.5 | 0.583 | |
| 4ban | M6S | Prothrombin | 3.4.21.5 | 0.583 | |
| 4baq | M4Z | Prothrombin | 3.4.21.5 | 0.583 | |
| 1ypj | UIB | Prothrombin | 3.4.21.5 | 0.579 | |
| 1t4u | 81A | Prothrombin | 3.4.21.5 | 0.578 | |
| 1zgv | 501 | Prothrombin | 3.4.21.5 | 0.574 | |
| 1jwt | BLI | Prothrombin | 3.4.21.5 | 0.573 | |
| 4bao | MVF | Prothrombin | 3.4.21.5 | 0.573 | |
| 2zhe | 13U | Prothrombin | 3.4.21.5 | 0.570 | |
| 1a4w | QWE | Prothrombin | 3.4.21.5 | 0.569 | |
| 1vzq | SHY | Prothrombin | 3.4.21.5 | 0.569 | |
| 3hat | GLY_VAL_ARG_RNG | Prothrombin | 3.4.21.5 | 0.568 | |
| 4az2 | 9MU | Prothrombin | 3.4.21.5 | 0.566 | |
| 1ype | UIP | Prothrombin | 3.4.21.5 | 0.562 | |
| 3qto | 10P | Prothrombin | 3.4.21.5 | 0.561 | |
| 2bvs | 2CE | Prothrombin | 3.4.21.5 | 0.559 | |
| 1k21 | IGN | Prothrombin | 3.4.21.5 | 0.557 | |
| 1nzq | 162 | Prothrombin | 3.4.21.5 | 0.556 | |
| 2r2m | I50 | Prothrombin | 3.4.21.5 | 0.554 | |
| 2cf9 | 348 | Prothrombin | 3.4.21.5 | 0.551 | |
| 3c27 | DKK | Prothrombin | 3.4.21.5 | 0.549 | |
| 1c4u | IH1 | Prothrombin | 3.4.21.5 | 0.548 | |
| 3p17 | 99P | Prothrombin | 3.4.21.5 | 0.547 | |
| 4rn6 | 15U | Prothrombin | 3.4.21.5 | 0.546 | |
| 4ayv | 9MQ | Prothrombin | 3.4.21.5 | 0.522 | |
| 3utu | 1TS | Prothrombin | 3.4.21.5 | 0.520 | |
| 3dhk | 23U | Prothrombin | 3.4.21.5 | 0.519 | |
| 3biv | 11U | Prothrombin | 3.4.21.5 | 0.510 | |
| 3qtv | 06P | Prothrombin | 3.4.21.5 | 0.509 | |
| 2gde | SN3 | Prothrombin | 3.4.21.5 | 0.507 | |
| 1riw | OSC | Prothrombin | 3.4.21.5 | 0.501 | |
| 5cmx | 0G6 | Prothrombin | 3.4.21.5 | 0.499 | |
| 1o0d | 163 | Prothrombin | 3.4.21.5 | 0.498 | |
| 1w7g | MIU | Prothrombin | 3.4.21.5 | 0.490 | |
| 1ny2 | ARG_PRO_PRO_GLY | Prothrombin | 3.4.21.5 | 0.488 | |
| 2ziq | 26U | Prothrombin | 3.4.21.5 | 0.483 | |
| 1c4v | IH2 | Prothrombin | 3.4.21.5 | 0.474 | |
| 1uvs | I11 | Prothrombin | 3.4.21.5 | 0.474 | |
| 1mu8 | CDB | Prothrombin | 3.4.21.5 | 0.471 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.469 | |
| 1uma | IN2 | Prothrombin | 3.4.21.5 | 0.467 | |
| 3qdz | PRO_ALA_PRO_ARG | Prothrombin | 3.4.21.5 | 0.464 | |
| 4bby | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.464 | |
| 3ada | NAD | Subunit alpha of sarocosine oxidase | / | 0.463 | |
| 1nuu | NAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.460 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.460 | |
| 2a2x | NA9 | Prothrombin | 3.4.21.5 | 0.460 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.460 | |
| 4loy | 6XS | Prothrombin | 3.4.21.5 | 0.459 | |
| 1ghv | 120 | Prothrombin | 3.4.21.5 | 0.457 | |
| 3dys | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.457 | |
| 3h59 | H59 | Genome polyprotein | 2.7.7.48 | 0.456 | |
| 2wu4 | HBP | Acetylcholinesterase | 3.1.1.7 | 0.455 | |
| 4uyf | 73B | Bromodomain-containing protein 2 | / | 0.454 | |
| 2fap | RAD | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.453 | |
| 2fap | RAD | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.453 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.452 | |
| 3eks | CY9 | Actin-5C | / | 0.452 | |
| 2gyw | OBI | Acetylcholinesterase | 3.1.1.7 | 0.451 | |
| 1q0r | AKT | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.450 | |
| 4bca | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.450 | |
| 1uyc | PU7 | Heat shock protein HSP 90-alpha | / | 0.448 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.447 | |
| 1mvt | DTM | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 3fbu | COA | Acetyltransferase, GNAT family | / | 0.447 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 4gxs | 0YS | Glutamate receptor 2 | / | 0.447 | |
| 4uug | PXG | Branched-chain amino acid aminotransferase, putative | / | 0.447 | |
| 1ju2 | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.446 | |
| 2vcm | M11 | Isopenicillin N synthase | 1.21.3.1 | 0.446 | |
| 3f68 | 91U | Prothrombin | 3.4.21.5 | 0.446 | |
| 3h1v | TK1 | Glucokinase | 2.7.1.2 | 0.445 | |
| 4b11 | 7I1 | Glycylpeptide N-tetradecanoyltransferase | / | 0.445 | |
| 4btt | VYR | Coagulation factor X | 3.4.21.6 | 0.445 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.444 | |
| 4f7i | NAD | 3-isopropylmalate dehydrogenase | 1.1.1.85 | 0.444 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.443 | |
| 1u1g | BBB | Uridine phosphorylase | 2.4.2.3 | 0.443 | |
| 2x7h | PFN | Prostaglandin reductase 3 | 1 | 0.443 | |
| 3ndj | JHZ | Methyltransferase | / | 0.443 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.442 | |
| 3br9 | DEY | Genome polyprotein | 2.7.7.48 | 0.442 | |
| 3eku | CY9 | Actin-5C | / | 0.442 | |
| 1yhj | R6C | Pyridoxal kinase | 2.7.1.35 | 0.441 | |
| 3e34 | ED1 | Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha | / | 0.441 | |
| 3e34 | ED1 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.441 | |
| 1kts | C24 | Prothrombin | 3.4.21.5 | 0.440 | |
| 2aq7 | TL5 | 3-oxoacyl-[acyl-carrier-protein] synthase 1 | 2.3.1.41 | 0.440 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.440 | |
| 3oqf | S51 | Renin | 3.4.23.15 | 0.440 | |
| 4b1j | A1R | Poly(ADP-ribose) glycohydrolase | 3.2.1.143 | 0.440 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.440 | |
| 4k8s | 1QT | Beta-secretase 1 | 3.4.23.46 | 0.440 |