FAIRMol

Z431946948

Pose ID 4407 Compound 2744 Pose 344

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
T07
T. brucei PTR1 T. brucei
Ligand Z431946948
PDB6RX6↗

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 strong SASA done
Strain ΔE
25.7 kcal/mol
Protein clashes
0
Internal clashes
12
Native overlap
contact recall 0.68, Jaccard 0.65, H-bond role recall 0.00
Burial
85%
Hydrophobic fit
97%
Reason: 12 internal clashes
12 intramolecular clashes
EcoTox / ADMET In-silico prediction only
Fish LC₅₀
Cat. 1 — Very toxic (≤1 mg/L)
Daphnia EC₅₀
Cat. 1 — Very toxic (≤1 mg/L)
Algae IC₅₀
Cat. 1 — Very toxic (≤1 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Medium Ames Clear DILI Risk
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.058 kcal/mol/HA) ✓ Good fit quality (FQ -9.87) ✓ Deep burial (85% SASA buried) ✓ Lipophilic contacts well-matched (97%) ✗ High strain energy (25.7 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (12)
Score
-28.566
kcal/mol
LE
-1.058
kcal/mol/HA
Fit Quality
-9.87
FQ (Leeson)
HAC
27
heavy atoms
MW
356
Da
LogP
4.98
cLogP
Final rank
0.4472
rank score
Inter norm
-1.134
normalised
Contacts
14
H-bonds 1
Strain ΔE
25.7 kcal/mol
SASA buried
85%
Lipo contact
97% BSA apolar/total
SASA unbound
641 Ų
Apolar buried
528 Ų

Interaction summary

HBD 1 HY 9 PI 5 CLASH 0

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 1.

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: strict.
NameTbPTR1_cW_6RX6_ReadyContacts19
PoseOpen native poseHB0
IFP residues
ARG14 ASP161 CYS168 GLY205 LEU208 LEU209 LYS178 MET213 NAP301 PHE171 PHE97 PRO210 PRO99 SER207 SER95 TRP221 TYR174 TYR98 VAL206
Current overlap13Native recall0.68
Jaccard0.65RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

Protein summary

275 residues
Protein targetT07Atoms3932
Residues275Chains3
Residue summaryLEU:437; VAL:433; ALA:361; ARG:288; ILE:266; GLU:210; LYS:198; SER:198; ASN:182; THR:154; GLN:153; PHE:140; PRO:140; TYR:126; GLY:112; HIS:103

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
A:NAP301

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
344 0.44718046292319397 -1.13414 -28.5659 1 14 13 0.68 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 -28.566kcal/mol
Ligand efficiency (LE) -1.0580kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.871
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 27HA

Physicochemical properties
Molecular weight 356.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.98
Lipinski: ≤ 5
Rotatable bonds 5

Conformational strain (MMFF94s)
Strain energy (ΔE) 25.74kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 157.82kcal/mol
Minimised FF energy 132.08kcal/mol

SASA & burial

✓ computed
SASA (unbound) 640.8Ų
Total solvent-accessible surface area of free ligand
BSA total 544.7Ų
Buried surface area upon binding
BSA apolar 528.3Ų
Hydrophobic contacts buried
BSA polar 16.4Ų
Polar contacts buried
Fraction buried 85.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 97.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1767.2Ų
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 2051.9Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 909.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)