FAIRMol

NMT-TY0602

Pose ID 3683 Compound 643 Pose 297

DB SELECTIONDocking 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 NMT-TY0602
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
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
51.8 kcal/mol
Protein clashes
2
Internal clashes
4
Native overlap
contact recall 0.71, Jaccard 0.65, H-bond role recall 0.25
Burial
97%
Hydrophobic fit
62%
Reason: strain 51.8 kcal/mol
strain ΔE 51.8 kcal/mol 2 protein-contact clashes 4 intramolecular clashes
EcoTox / ADMET GDS: UNSAFE UL GreenDrugScore ML model
ECOscore
0.957
aquatic tox · BCF · biodeg.
GDS₃ (3-block)
0.580
ADMET + ECO + DL
ADMETscore (GDS)
0.560
absorption · distr. · metab.
DLscore
0.393
drug-likeness
P(SAFE)
0.05
GDS classification
ADMET alerts (in-silico)
hERG Low Ames Clear DILI Low
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.684 kcal/mol/HA) ✓ Good fit quality (FQ -6.13) ✓ Deep burial (97% SASA buried) ✓ Lipophilic contacts well-matched (62%) ✗ Extreme strain energy (51.8 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (9)
Score
-16.409
kcal/mol
LE
-0.684
kcal/mol/HA
Fit Quality
-6.13
FQ (Leeson)
HAC
24
heavy atoms
MW
371
Da
LogP
-0.09
cLogP
Final rank
3.2485
rank score
Inter norm
-0.969
normalised
Contacts
17
H-bonds 6
Strain ΔE
51.8 kcal/mol
SASA buried
97%
Lipo contact
62% BSA apolar/total
SASA unbound
571 Ų
Apolar buried
341 Ų

Interaction summary

HBA 2 PC 1 HY 7 PI 2 CLASH 4

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

PC · Polar contacts (possible, no H geometry)
HBD?/HBA? — heavy-atom distance only, H geometry unavailable. May be real H-bonds.

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.
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 overlap15Native recall0.71
Jaccard0.65RMSD-
HB strict1Strict recall0.20
HB same residue+role1HB role recall0.25
HB same residue2HB residue recall0.50

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
345 2.3852300086674956 -1.22883 -27.1471 9 14 1 0.05 0.00 - no Open
314 2.517801636797984 -0.942176 -24.1381 5 13 0 0.00 0.00 - no Open
272 2.9189537056135753 -1.1672 -29.7247 13 13 0 0.00 0.00 - no Open
414 3.1764200655621546 -1.06469 -24.8485 7 16 0 0.00 0.00 - no Open
297 3.248504433051989 -0.969391 -16.4093 6 17 15 0.71 0.25 - no Current
274 3.710791772393639 -1.07629 -24.7513 9 15 1 0.05 0.00 - no Open
383 3.8800478154472353 -1.20228 -28.5869 11 16 0 0.00 0.00 - no Open
258 4.050558324957515 -1.18293 -28.8656 12 22 0 0.00 0.00 - no Open
259 4.168971048980509 -1.13785 -26.3976 11 13 0 0.00 0.00 - no Open
364 4.531136784780454 -1.24281 -28.4071 7 15 0 0.00 0.00 - no Open
247 4.9387540833797265 -1.05098 -20.2639 12 13 0 0.00 0.00 - no Open
285 5.825536396152312 -1.3346 -31.8099 16 21 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 -16.409kcal/mol
Ligand efficiency (LE) -0.6837kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -6.127
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 24HA

Physicochemical properties
Molecular weight 371.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) -0.09
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 51.78kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -22.74kcal/mol
Minimised FF energy -74.52kcal/mol

SASA & burial

✓ computed
SASA (unbound) 570.7Ų
Total solvent-accessible surface area of free ligand
BSA total 555.2Ų
Buried surface area upon binding
BSA apolar 341.2Ų
Hydrophobic contacts buried
BSA polar 214.0Ų
Polar contacts buried
Fraction buried 97.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 61.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1576.9Ų
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 575.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)