FAIRMol

Z57100312

Pose ID 5129 Compound 3119 Pose 388

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
T08
T. brucei PTR1 T. brucei
Ligand Z57100312
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
25.4 kcal/mol
Protein clashes
7
Internal clashes
9
Native overlap
contact recall 0.63, Jaccard 0.52, H-bond role recall 0.80
Burial
96%
Hydrophobic fit
83%
Reason: 9 internal clashes
7 protein-contact clashes 9 intramolecular clashes
EcoTox / ADMET In-silico prediction only
Fish LC₅₀
Cat. 3 — Harmful (10–100 mg/L)
Daphnia EC₅₀
Cat. 3 — Harmful (10–100 mg/L)
Algae IC₅₀
Cat. 3 — Harmful (10–100 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Medium Ames Clear DILI Low
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.311 kcal/mol/HA) ✓ Good fit quality (FQ -11.75) ✓ Good H-bonds (4 bonds) ✓ Deep burial (96% SASA buried) ✓ Lipophilic contacts well-matched (83%) ✗ High strain energy (25.4 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)
Score
-31.469
kcal/mol
LE
-1.311
kcal/mol/HA
Fit Quality
-11.75
FQ (Leeson)
HAC
24
heavy atoms
MW
320
Da
LogP
2.52
cLogP
Final rank
2.0596
rank score
Inter norm
-1.433
normalised
Contacts
16
H-bonds 8
Strain ΔE
25.4 kcal/mol
SASA buried
96%
Lipo contact
83% BSA apolar/total
SASA unbound
586 Ų
Apolar buried
468 Ų

Interaction summary

HBD 4 HY 8 PI 2 CLASH 9

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 4.

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

HY · Hydrophobic contacts

CLASH · Clashes

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 overlap12Native recall0.63
Jaccard0.52RMSD-
HB strict3Strict recall0.50
HB same residue+role4HB role recall0.80
HB same residue4HB residue recall0.80

Protein summary

258 residues
Protein targetT08Atoms3881
Residues258Chains2
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
388 2.0596268193866436 -1.43345 -31.4693 8 16 12 0.63 0.80 - no Current
373 2.7108674867594806 -1.34006 -29.1891 8 18 0 0.00 0.00 - no Open
350 4.2983685017773885 -1.10054 -26.4883 12 14 0 0.00 0.00 - no Open

Molecular metrics

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

Scoring & efficiency
Docking score -31.469kcal/mol
Ligand efficiency (LE) -1.3112kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -11.751
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 24HA

Physicochemical properties
Molecular weight 320.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.52
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 25.39kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 162.75kcal/mol
Minimised FF energy 137.36kcal/mol

SASA & burial

✓ computed
SASA (unbound) 586.1Ų
Total solvent-accessible surface area of free ligand
BSA total 560.8Ų
Buried surface area upon binding
BSA apolar 467.6Ų
Hydrophobic contacts buried
BSA polar 93.1Ų
Polar contacts buried
Fraction buried 95.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 83.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1600.2Ų
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 938.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)