URODY311CpathogenicCOMPLETEPCD-UROD-Y311C

Hepatoerythropoietic porphyria

Pathogenic missense — mechanism TBD

UniProt P06132ClinVar #71Precursor Y311C
fpocket Druggability0.902
Chaperone Composite0.842
Pocket Affinity0.758
Drug-likeness (QED)0.678
Stage 2 — Transient Pocket

Cryptic Binding Site

0.902
fpocket Drug.
0.752
WT Baseline
501.7
Volume (ų)
42
α-Spheres
20
Conformations
3.4 Å
Mut→Pocket Dist.
Pocket Type
Cryptic
Pocket Center (Å)
(-20.0, 8.9, -2.9)
Pocket-Lining Residues
C308A309L310Y311A312S313E314E316I317M345D346H349V350A352
Sequence Slice (±20 aa around pocket)
LQGNLDPCALYASEEEIGQLV
3D Structure
Transient pocket conformation · drag to rotate
Loading structure

ANM-sampled transient conformation

Stage 3 — De Novo Chaperone

REFOLD-UROD-Y311C-C1

SMILES String
NS(=O)(=O)c1ccncc1N1CCCCC1CNC(=O)c1ccncc1N1CCCCC1
Physicochemical Properties
458
MW (Da)
1.90
logP
0.678
QED
3.2
SA
2
HBD
7
HBA
122
TPSA (Ų)
Drug-likeness Rules
✓ Lipinski Ro5
✓ Veber Oral
✓ PAINS-free
Predicted Binding Mode
salt bridge
E314, E316, D346
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 14 × 14Source /Users/TheAES/Desktop/REFOLD/data/results/UROD_Y311C/E_ij_matrix.npy
C308A309L310Y311A312S313E314E316I317M345D346H349V350A352
C308
0.0
3.9
5.2
5.6
7.8
11.3
12.6
11.9
10.1
8.4
11.0
10.8
11.1
13.7
A309
3.9
0.0
3.9
5.4
5.6
8.8
9.7
8.2
6.4
10.0
11.4
9.4
10.2
11.3
L310
5.2
3.9
0.0
3.9
5.3
7.6
7.9
8.8
6.3
6.9
7.7
5.8
6.9
8.7
Y311
5.6
5.4
3.9
0.0
3.8
6.7
8.8
9.5
8.5
6.7
7.6
7.6
9.8
11.3
A312
7.8
5.6
5.3
3.8
0.0
3.8
6.6
5.9
6.2
10.2
10.1
8.2
11.0
10.6
S313
11.3
8.8
7.6
6.7
3.8
0.0
3.9
5.2
6.2
11.8
10.4
7.6
11.1
9.2
E314
12.6
9.7
7.9
8.8
6.6
3.9
0.0
5.6
5.0
12.3
10.4
6.0
9.1
5.7
E316
11.9
8.2
8.8
9.5
5.9
5.2
5.6
0.0
3.9
15.0
14.3
10.2
12.6
9.8
I317
10.1
6.4
6.3
8.5
6.2
6.2
5.0
3.9
0.0
12.8
12.2
7.7
9.3
6.9
M345
8.4
10.0
6.9
6.7
10.2
11.8
12.3
15.0
12.8
0.0
3.8
7.6
8.0
12.1
D346
11.0
11.4
7.7
7.6
10.1
10.4
10.4
14.3
12.2
3.8
0.0
5.4
6.8
10.0
H349
10.8
9.4
5.8
7.6
8.2
7.6
6.0
10.2
7.7
7.6
5.4
0.0
3.9
4.8
V350
11.1
10.2
6.9
9.8
11.0
11.1
9.1
12.6
9.3
8.0
6.8
3.9
0.0
5.5
A352
13.7
11.3
8.7
11.3
10.6
9.2
5.7
9.8
6.9
12.1
10.0
4.8
5.5
0.0
0 Å
15 Å
Sequence

Full Protein Sequence

>UROD_Y311C | REFOLD PCD entry

MEANGLGPQGFPELKNDTFLRAAWGEETDYTPVWCMRQAGRYLPEFRETRAAQDFFSTCRSPEACCELTLQPLRRFPLDAAIIFSDILVVPQALGMEVTMVPGKGPSFPEPLREEQDLERLRDPEVVASELGYVFQAITLTRQRLAGRVPLIGFAGAPWTLMTYMVEGGGSSTMAQAKRWLYQRPQASHQLLRILTDALVPYLVGQVVAGAQALQLFESHAGHLGPQLFNKFALPYIRDVAKQVKARLREAGLAPVPMIIFAKDGHFALEELAQAGYEVVGLDWTVAPKKARECVGKTVTLQGNLDPCALYASEEEIGQLVKQMLDDFGPHRYIANLGHGLYPDMDPEHVGAFVDAVHKHSRLLRQN
Pocket-lining residues: CALYASEEIMDHVA
Data Assets

Downloadable Files

E_ij Matrix (.npy)
/Users/TheAES/Desktop/REFOLD/data/results/UROD_Y311C/E_ij_matrix.npy
E_ij Matrix (.csv)
/Users/TheAES/Desktop/REFOLD/data/results/UROD_Y311C/E_ij_matrix.csv
Transient Conformation (.pdb)
/Users/TheAES/Desktop/REFOLD/data/results/UROD_Y311C/conformations/mt_01.pdb
Pocket Summary (.json)
/Users/TheAES/Desktop/REFOLD/data/results/UROD_Y311C/pocket_summary.json
Stage 3 Candidates (.json)
/Users/TheAES/Desktop/REFOLD/data/results/UROD_Y311C/stage3_chaperone_candidates.json
← Back to Database
REFOLD · S.Y.A.L.I.S Labs · Aaryan Senthilvanan