FAIRMol

ulfkktlib_2811

Pose ID 12439 Compound 5138 Pose 238

DB fairmolDocking pose analysis is being read from this database.
Compound detail Protein structures Back to compounds
Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
T19
T. brucei TR (NADPH binding site) T. brucei NADPH binding site
Ligand ulfkktlib_2811
PDB2WOV↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native mixed SASA done
Strain ΔE
17.9 kcal/mol
Protein clashes
0
Internal clashes
14
Native overlap
contact recall 0.26, Jaccard 0.19, H-bond role recall 0.00
Burial
95%
Hydrophobic fit
81%
Reason: 14 internal clashes
14 intramolecular clashes
EcoTox / ADMET In-silico prediction only
Fish LC₅₀
Not classified (>100 mg/L)
Daphnia EC₅₀
Not classified (>100 mg/L)
Algae IC₅₀
Cat. 3 — Harmful (10–100 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Low Ames Clear DILI Low
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.477 kcal/mol/HA) ✓ Good fit quality (FQ -12.36) ✓ Good H-bonds (3 bonds) ✓ Deep burial (95% SASA buried) ✓ Lipophilic contacts well-matched (81%) ✗ Moderate strain (17.9 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (14)
Score
-29.548
kcal/mol
LE
-1.477
kcal/mol/HA
Fit Quality
-12.36
FQ (Leeson)
HAC
20
heavy atoms
MW
268
Da
LogP
2.08
cLogP
Final rank
2.9432
rank score
Inter norm
-1.551
normalised
Contacts
16
H-bonds 4
Strain ΔE
17.9 kcal/mol
SASA buried
95%
Lipo contact
81% BSA apolar/total
SASA unbound
477 Ų
Apolar buried
365 Ų

Interaction summary

HBD 1 HBA 2 HY 7 PI 2 CLASH 0

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 3.

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes
No clash · clashes detected for this pose.

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
Name2WOVContacts27
PoseOpen native poseHB0
IFP residues
ALA284 ALA365 ARG222 ARG228 ARG287 ASN223 ASN254 GLN165 GLU202 GLY195 GLY196 GLY197 GLY286 ILE199 ILE285 LEU227 LEU334 LYS60 MET333 NDP800 PHE198 PHE367 PRO167 SER200 TYR221 VAL194 VAL366
Current overlap7Native recall0.26
Jaccard0.19RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

Protein summary

493 residues
Protein targetT19Atoms7541
Residues493Chains1
Residue summaryVAL:768; LYS:704; LEU:703; ILE:532; GLU:450; THR:434; ARG:408; PHE:400; ALA:390; ASN:350; PRO:350; GLY:336; SER:330; TYR:294; ASP:264; MET:221

Receptor context

1 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 1 Excluded HETATM 0
Kept cofactors / ions
C:NDP800

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
238 2.9431621378231867 -1.55089 -29.5477 4 16 7 0.26 0.00 - no Current

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
✓ Metrics available

Scoring & efficiency
Docking score -29.548kcal/mol
Ligand efficiency (LE) -1.4774kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -12.363
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 20HA

Physicochemical properties
Molecular weight 268.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.08
Lipinski: ≤ 5
Rotatable bonds 3

Conformational strain (MMFF94s)
Strain energy (ΔE) 17.92kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 40.45kcal/mol
Minimised FF energy 22.53kcal/mol

SASA & burial

✓ computed
SASA (unbound) 476.8Ų
Total solvent-accessible surface area of free ligand
BSA total 450.9Ų
Buried surface area upon binding
BSA apolar 365.4Ų
Hydrophobic contacts buried
BSA polar 85.6Ų
Polar contacts buried
Fraction buried 94.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 81.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2984.4Ų
SASA_nonpolar(complex) − SASA_nonpolar(receptor) − SASA_nonpolar(ligand free). Negative = non-polar surface buried upon binding. Requires full polarity-decomposed SASA computation.
Receptor non-polar SASA 4064.7Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1471.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)