FAIRMol

NMT-TY0910

Pose ID 2377 Compound 1778 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
T04
L. major PTR1 L. major
Ligand NMT-TY0910
PDB7PXX↗

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
29.3 kcal/mol
Protein clashes
2
Internal clashes
3
Native overlap
contact recall 0.58, Jaccard 0.58, H-bond role recall 0.60
Burial
86%
Hydrophobic fit
56%
Reason: no major geometry red flags detected
2 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 (-1.334 kcal/mol/HA) ✓ Good fit quality (FQ -10.93) ✓ Deep burial (86% SASA buried) ✗ High strain energy (29.3 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (6)
Score
-25.341
kcal/mol
LE
-1.334
kcal/mol/HA
Fit Quality
-10.93
FQ (Leeson)
HAC
19
heavy atoms
MW
282
Da
LogP
-0.14
cLogP
Final rank
1.2093
rank score
Inter norm
-1.315
normalised
Contacts
11
H-bonds 5
Strain ΔE
29.3 kcal/mol
SASA buried
86%
Lipo contact
56% BSA apolar/total
SASA unbound
475 Ų
Apolar buried
230 Ų

Interaction summary

HBA 1 HY 4 PI 3 CLASH 3

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

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name7PXXContacts19
PoseOpen native poseHB0
IFP residues
ARG17 ASP181 GLY225 HIS241 LEU188 LEU226 LEU229 LYS198 MET233 NDP302 PHE113 PRO115 SER111 SER112 SER227 TYR191 TYR194 VAL230 ARG287
Current overlap11Native recall0.58
Jaccard0.58RMSD-
HB strict3Strict recall0.50
HB same residue+role3HB role recall0.60
HB same residue3HB residue recall0.60

Protein summary

308 residues
Protein targetT04Atoms4210
Residues308Chains3
Residue summaryLEU:494; ALA:421; ARG:384; VAL:368; THR:295; TYR:231; SER:198; PRO:196; ILE:190; LYS:176; ASN:154; GLU:150; GLY:126; PHE:120; HIS:119; ASP:108

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:NDP302

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
344 1.2093337204826755 -1.31499 -25.3409 5 11 11 0.58 0.60 - no Current
341 2.594542948923521 -1.14854 -21.6812 8 13 0 0.00 0.00 - no Open
284 3.950465520677434 -1.43928 -27.3002 9 17 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 -25.341kcal/mol
Ligand efficiency (LE) -1.3337kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.932
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 19HA

Physicochemical properties
Molecular weight 282.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) -0.14
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 29.26kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -169.60kcal/mol
Minimised FF energy -198.86kcal/mol

SASA & burial

✓ computed
SASA (unbound) 475.4Ų
Total solvent-accessible surface area of free ligand
BSA total 409.4Ų
Buried surface area upon binding
BSA apolar 229.7Ų
Hydrophobic contacts buried
BSA polar 179.7Ų
Polar contacts buried
Fraction buried 86.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 56.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1452.9Ų
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 2179.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1011.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)