FAIRMol

NMT-TY0142

Pose ID 9128 Compound 4144 Pose 320

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
T14
T. brucei ODC (G418 binding site) T. brucei G418 binding site
Ligand NMT-TY0142
PDB1NJJ↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising SASA cached
Promising and worth follow-up
Binding strong Geometry high Native mixed SASA done
Strain ΔE
12.5 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.40, Jaccard 0.32, H-bond role recall 0.20
Burial
87%
Hydrophobic fit
60%
Reason: no major geometry red flags detected
2 protein-contact clashes 43% of hydrophobic surface appears solvent-exposed (3/7 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.545 kcal/mol/HA) ✓ Good fit quality (FQ -11.05) ✓ Good H-bonds (5 bonds) ✓ Deep burial (87% SASA buried) ✗ Moderate strain (12.5 kcal/mol) ✗ Geometry warnings
Score
-21.635
kcal/mol
LE
-1.545
kcal/mol/HA
Fit Quality
-11.05
FQ (Leeson)
HAC
14
heavy atoms
MW
214
Da
LogP
-0.95
cLogP
Strain ΔE
12.5 kcal/mol
SASA buried
87%
Lipo contact
60% BSA apolar/total
SASA unbound
372 Ų
Apolar buried
193 Ų

Interaction summary

HB 5 HY 5 PI 0 CLASH 2 ⚠ Exposure 42%
⚠️Partial hydrophobic solvent exposure
43% of hydrophobic surface appears solvent-exposed (3/7 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 7 Buried (contacted) 4 Exposed 3 LogP -0.95 H-bonds 5
Exposed fragments: aromatic ring (3/6 atoms exposed)
Final rank2.448Score-21.635
Inter norm-1.563Intra norm0.017
Top1000noExcludedno
Contacts10H-bonds5
Artifact reasongeometry warning; 4 clashes; 2 protein clashes
Residues
ARG337 ASP243 ASP385 GLU384 LEU339 MET386 PHE383 THR241 VAL335 VAL336

Protein summary

398 residues
Protein targetT14Atoms6140
Residues398Chains1
Residue summaryVAL:592; LEU:513; LYS:484; ARG:432; PHE:420; ILE:418; ASP:349; THR:322; TYR:315; PRO:308; GLU:301; ALA:290; SER:253; GLY:217; ASN:210; GLN:170

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:ORX602

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name1NJJContacts15
PoseOpen native poseHB0
IFP residues
ARG22 ARG242 ARG337 ARG342 ASP243 ASP385 GLN341 GLU384 LEU25 LEU339 LEU382 PRO340 PRO344 SER282 THR241
Current overlap6Native recall0.40
Jaccard0.32RMSD-
HB strict1Strict recall0.17
HB same residue+role1HB role recall0.20
HB same residue1HB residue recall0.20

HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

PI · π–π interactions
No pi · π–π interactions detected for this pose.

HY · Hydrophobic contacts

CLASH · Clashes

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
320 2.4481860142742238 -1.56271 -21.6348 5 10 6 0.40 0.20 - 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 -21.635kcal/mol
Ligand efficiency (LE) -1.5453kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -11.049
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 14HA

Physicochemical properties
Molecular weight 214.2Da
Lipinski: ≤ 500 Da
LogP (cLogP) -0.95
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 12.50kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -23.72kcal/mol
Minimised FF energy -36.22kcal/mol

SASA & burial

✓ computed
SASA (unbound) 372.1Ų
Total solvent-accessible surface area of free ligand
BSA total 322.2Ų
Buried surface area upon binding
BSA apolar 192.6Ų
Hydrophobic contacts buried
BSA polar 129.5Ų
Polar contacts buried
Fraction buried 86.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 59.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2212.9Ų
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 3349.0Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 1367.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)