FAIRMol

NMT-TY0549

Pose ID 7702 Compound 411 Pose 250

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
T12
T. brucei R5P T. brucei
Ligand NMT-TY0549
PDB6FXS↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak SASA cached
Weak or marginal quality
Binding strong Geometry medium Native strong SASA done
Strain ΔE
35.4 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 1.00, Jaccard 0.94, H-bond role recall 0.60
Burial
71%
Hydrophobic fit
57%
Reason: no major geometry red flags detected
3 protein-contact clashes 3 intramolecular clashes
EcoTox / ADMET In-silico prediction only
Fish LC₅₀
Not classified (>100 mg/L)
Daphnia EC₅₀
Not classified (>100 mg/L)
Algae IC₅₀
Not classified (>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 (-1.336 kcal/mol/HA) ✓ Good fit quality (FQ -12.46) ✓ Strong H-bond network (11 bonds) ✓ Deep burial (71% SASA buried) ✗ Very high strain energy (35.4 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)
Score
-36.062
kcal/mol
LE
-1.336
kcal/mol/HA
Fit Quality
-12.46
FQ (Leeson)
HAC
27
heavy atoms
MW
395
Da
LogP
-1.19
cLogP
Final rank
4.9265
rank score
Inter norm
-1.286
normalised
Contacts
17
H-bonds 15
Strain ΔE
35.4 kcal/mol
SASA buried
71%
Lipo contact
57% BSA apolar/total
SASA unbound
650 Ų
Apolar buried
263 Ų

Interaction summary

HBD 3 HBA 8 HY 3 PI 3 CLASH 3

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 8.

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.
Name6FXSContacts16
PoseOpen native poseHB0
IFP residues
ARG140 ARG144 ASN106 HIS105 HIS141 ARG46 ASP13 CYS72 GLY73 GLY75 GLY77 HIS14 ILE15 ILE76 SER74 TYR49
Current overlap16Native recall1.00
Jaccard0.94RMSD-
HB strict8Strict recall0.67
HB same residue+role6HB role recall0.60
HB same residue9HB residue recall0.90

Protein summary

302 residues
Protein targetT12Atoms4598
Residues302Chains2
Residue summaryARG:576; ILE:456; VAL:448; GLU:360; ALA:340; LEU:304; TYR:252; HIS:204; PRO:196; THR:196; GLY:182; LYS:176; ASP:168; PHE:160; MET:153; SER:121

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:CSD72

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
263 1.9619591920682486 -1.07778 -26.3261 11 17 0 0.00 0.00 - no Open
307 1.973236208634677 -0.911074 -24.9818 7 15 0 0.00 0.00 - no Open
270 2.217204642698369 -1.21946 -32.7493 11 15 0 0.00 0.00 - no Open
352 2.4054056429997805 -0.963314 -22.8123 12 19 0 0.00 0.00 - no Open
276 2.4644015191207718 -1.23884 -34.4996 16 21 0 0.00 0.00 - no Open
287 2.4692123455684767 -0.887788 -22.8583 6 18 0 0.00 0.00 - no Open
293 2.5523531210354715 -1.25212 -32.8271 13 20 0 0.00 0.00 - no Open
264 3.2494165124044274 -1.31147 -36.2843 14 18 0 0.00 0.00 - no Open
377 3.300748553183803 -0.898096 -26.0956 7 13 0 0.00 0.00 - no Open
324 3.301523972802756 -0.915736 -26.3877 13 13 0 0.00 0.00 - no Open
239 4.313905727494139 -1.00534 -29.1414 16 16 5 0.31 0.40 - no Open
273 4.418567444093437 -1.2144 -31.3287 15 26 0 0.00 0.00 - no Open
284 4.844348523444292 -1.06372 -30.1625 10 15 0 0.00 0.00 - no Open
250 4.926468000366607 -1.2862 -36.0618 15 17 16 1.00 0.60 - 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 -36.062kcal/mol
Ligand efficiency (LE) -1.3356kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -12.461
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 27HA

Physicochemical properties
Molecular weight 395.4Da
Lipinski: ≤ 500 Da
LogP (cLogP) -1.19
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 35.38kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -158.07kcal/mol
Minimised FF energy -193.45kcal/mol

SASA & burial

✓ computed
SASA (unbound) 650.3Ų
Total solvent-accessible surface area of free ligand
BSA total 462.6Ų
Buried surface area upon binding
BSA apolar 262.9Ų
Hydrophobic contacts buried
BSA polar 199.7Ų
Polar contacts buried
Fraction buried 71.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 56.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2083.4Ų
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 2454.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 794.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)