FAIRMol

Z19287096

Pose ID 4040 Compound 2499 Pose 654

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
T06
T. brucei DHFR T. brucei
Ligand Z19287096
PDB8RHT↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Likely artefact or unreliable pose
Binding strong Geometry medium Native strong SASA done
Strain ΔE
31.8 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.81, Jaccard 0.68, H-bond role recall 0.00
Burial
94%
Hydrophobic fit
75%
Reason: no major geometry red flags detected
5 protein-contact clashes 5 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
Yes
ADMET alerts (in-silico)
hERG High Ames Clear DILI Risk
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.478 kcal/mol/HA) ✓ Good fit quality (FQ -4.74) ✓ Deep burial (94% SASA buried) ✓ Lipophilic contacts well-matched (75%) ✗ Very high strain energy (31.8 kcal/mol) ✗ Geometry warnings ✗ Protein-contact clashes (6) ✗ Many internal clashes (10)
Score
-15.766
kcal/mol
LE
-0.478
kcal/mol/HA
Fit Quality
-4.74
FQ (Leeson)
HAC
33
heavy atoms
MW
462
Da
LogP
5.41
cLogP
Final rank
1.1735
rank score
Inter norm
-0.847
normalised
Contacts
21
H-bonds 1
Strain ΔE
31.8 kcal/mol
SASA buried
94%
Lipo contact
75% BSA apolar/total
SASA unbound
757 Ų
Apolar buried
532 Ų

Interaction summary

HBD 1 HY 10 PI 5 CLASH 5

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

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
Name8RHTContacts21
PoseOpen native poseHB0
IFP residues
ALA34 ASP54 HIS182 ILE160 ILE47 LEU90 LEU97 MET55 NDP301 PHE233 PHE58 PHE94 PRO91 SER89 THR184 THR86 TRP49 TYR166 TYR57 VAL32 VAL33
Current overlap17Native recall0.81
Jaccard0.68RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue0HB residue recall0.00

Protein summary

223 residues
Protein targetT06Atoms3452
Residues223Chains1
Residue summaryARG:408; VAL:352; LYS:308; LEU:304; PRO:238; ILE:209; GLU:195; THR:182; SER:176; ALA:160; PHE:140; ASN:126; GLY:126; ASP:108; GLN:85; NDP:74

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:NDP301

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
654 1.173501566040526 -0.84665 -15.7661 1 21 17 0.81 0.00 - no Current
666 2.4417895331946147 -0.605392 -12.9977 5 9 0 0.00 0.00 - no Open
668 3.4343533377078903 -0.62467 -20.105 8 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 -15.766kcal/mol
Ligand efficiency (LE) -0.4778kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -4.740
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 33HA

Physicochemical properties
Molecular weight 461.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 5.41
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 31.80kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 67.89kcal/mol
Minimised FF energy 36.09kcal/mol

SASA & burial

✓ computed
SASA (unbound) 757.2Ų
Total solvent-accessible surface area of free ligand
BSA total 710.6Ų
Buried surface area upon binding
BSA apolar 531.9Ų
Hydrophobic contacts buried
BSA polar 178.7Ų
Polar contacts buried
Fraction buried 93.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 74.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1793.0Ų
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 1808.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 591.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)