URODR292GpathogenicCOMPLETEPCD-UROD-R292G
Hepatoerythropoietic porphyria
Pathogenic missense — mechanism TBD
UniProt P06132ClinVar #69Precursor R292G
fpocket Druggability0.794
Chaperone Composite0.707
Pocket Affinity0.636
Drug-likeness (QED)0.774
Stage 2 — Transient Pocket
Cryptic Binding Site
0.794
fpocket Drug.
0.644
WT Baseline
537.8
Volume (ų)
24
α-Spheres
20
Conformations
4.7 Å
Mut→Pocket Dist.
Pocket Type
Cryptic
Pocket Center (Å)
(-13.6, -15.6, 2.8)
Pocket-Lining Residues
A287P288K289K290A291R292E293C294
Sequence Slice (±20 aa around pocket)
LDWTVAPKKARECVGKTVTLQ
3D Structure
Transient pocket conformation · drag to rotate
Loading structure
ANM-sampled transient conformation
Stage 3 — De Novo Chaperone
REFOLD-UROD-R292G-C1
SMILES String
COC1CCCC(N2CCCCC2)N1c1cnccc1NCCC(N)=O
Physicochemical Properties
361
MW (Da)
2.14
logP
0.774
QED
3.6
SA
2
HBD
6
HBA
84
TPSA (Ų)
Drug-likeness Rules
✓ Lipinski Ro5
✓ Veber Oral
✓ PAINS-free
Predicted Binding Mode
salt bridge
K289, K290, R292, E293
Stage 2 Output
Eᴵʲ Pairwise Distance Matrix
Cα–Cα distances (Å) between pocket-lining residues in the selected transient conformation. Used as conditioning input for Stage 3 pharmacophore-guided SMILES generation.
Shape 8 × 8Source /Users/TheAES/Desktop/REFOLD/data/results/UROD_R292G/E_ij_matrix.npy
| A287 | P288 | K289 | K290 | A291 | R292 | E293 | C294 | |
|---|---|---|---|---|---|---|---|---|
| A287 | 0.0 | 3.9 | 5.7 | 5.4 | 6.3 | 8.8 | 10.1 | 10.8 |
| P288 | 3.9 | 0.0 | 3.9 | 5.5 | 5.0 | 6.2 | 8.7 | 10.0 |
| K289 | 5.7 | 3.9 | 0.0 | 3.9 | 5.4 | 5.1 | 6.3 | 8.9 |
| K290 | 5.4 | 5.5 | 3.9 | 0.0 | 3.8 | 5.4 | 4.9 | 6.3 |
| A291 | 6.3 | 5.0 | 5.4 | 3.8 | 0.0 | 3.9 | 5.4 | 5.2 |
| R292 | 8.8 | 6.2 | 5.1 | 5.4 | 3.9 | 0.0 | 3.9 | 5.5 |
| E293 | 10.1 | 8.7 | 6.3 | 4.9 | 5.4 | 3.9 | 0.0 | 3.9 |
| C294 | 10.8 | 10.0 | 8.9 | 6.3 | 5.2 | 5.5 | 3.9 | 0.0 |
0 Å
11 Å
Sequence
Full Protein Sequence
>UROD_R292G | REFOLD PCD entry
MEANGLGPQGFPELKNDTFLRAAWGEETDYTPVWCMRQAGRYLPEFRETRAAQDFFSTCRSPEACCELTLQPLRRFPLDAAIIFSDILVVPQALGMEVTMVPGKGPSFPEPLREEQDLERLRDPEVVASELGYVFQAITLTRQRLAGRVPLIGFAGAPWTLMTYMVEGGGSSTMAQAKRWLYQRPQASHQLLRILTDALVPYLVGQVVAGAQALQLFESHAGHLGPQLFNKFALPYIRDVAKQVKARLREAGLAPVPMIIFAKDGHFALEELAQAGYEVVGLDWTVAPKKARECVGKTVTLQGNLDPCALYASEEEIGQLVKQMLDDFGPHRYIANLGHGLYPDMDPEHVGAFVDAVHKHSRLLRQN
Pocket-lining residues: APKKAREC
Data Assets
Downloadable Files
E_ij Matrix (.npy)
/Users/TheAES/Desktop/REFOLD/data/results/UROD_R292G/E_ij_matrix.npy
E_ij Matrix (.csv)
/Users/TheAES/Desktop/REFOLD/data/results/UROD_R292G/E_ij_matrix.csv
Transient Conformation (.pdb)
/Users/TheAES/Desktop/REFOLD/data/results/UROD_R292G/conformations/mt_01.pdb
Pocket Summary (.json)
/Users/TheAES/Desktop/REFOLD/data/results/UROD_R292G/pocket_summary.json
Stage 3 Candidates (.json)
/Users/TheAES/Desktop/REFOLD/data/results/UROD_R292G/stage3_chaperone_candidates.json
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REFOLD · S.Y.A.L.I.S Labs · Aaryan Senthilvanan