FAIRMol

NMT-TY0139

Pose ID 4346 Compound 1819 Pose 283

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
T07
T. brucei PTR1 T. brucei
Ligand NMT-TY0139
PDB6RX6↗

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
17.6 kcal/mol
Protein clashes
0
Internal clashes
1
Native overlap
contact recall 0.53, Jaccard 0.53, H-bond role recall 0.40
Burial
96%
Hydrophobic fit
48%
Reason: no major geometry red flags detected
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.935 kcal/mol/HA) ✓ Good fit quality (FQ -14.30) ✓ Strong H-bond network (7 bonds) ✓ Deep burial (96% SASA buried) ✗ Moderate strain (17.6 kcal/mol) ✗ Geometry warnings
Score
-29.031
kcal/mol
LE
-1.935
kcal/mol/HA
Fit Quality
-14.30
FQ (Leeson)
HAC
15
heavy atoms
MW
225
Da
LogP
-0.85
cLogP
Strain ΔE
17.6 kcal/mol
SASA buried
96%
Lipo contact
48% BSA apolar/total
SASA unbound
371 Ų
Apolar buried
171 Ų

Interaction summary

HB 7 HY 8 PI 2 CLASH 1

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

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes
Final rank-1.432Score-29.031
Inter norm-2.020Intra norm0.085
Top1000noExcludedno
Contacts10H-bonds7
Artifact reasongeometry warning; 2 clashes; 1 protein contact clash; 5 cofactor-context clashes
Residues
ARG14 ASP161 CYS168 LEU208 LEU209 NAP301 PHE97 PRO210 SER95 TYR174

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
NameTbPTR1_cW_6RX6_ReadyContacts19
PoseOpen native poseHB0
IFP residues
ARG14 ASP161 CYS168 GLY205 LEU208 LEU209 LYS178 MET213 NAP301 PHE171 PHE97 PRO210 PRO99 SER207 SER95 TRP221 TYR174 TYR98 VAL206
Current overlap10Native recall0.53
Jaccard0.53RMSD-
HB strict2Strict recall0.33
HB same residue+role2HB role recall0.40
HB same residue3HB residue recall0.60

Protein summary

275 residues
Protein targetT07Atoms3932
Residues275Chains3
Residue summaryLEU:437; VAL:433; ALA:361; ARG:288; ILE:266; GLU:210; LYS:198; SER:198; ASN:182; THR:154; GLN:153; PHE:140; PRO:140; TYR:126; GLY:112; HIS:103

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:NAP301

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
283 -1.43235038960848 -2.02036 -29.0308 7 10 10 0.53 0.40 - no Current
251 1.2396203427272454 -1.91109 -30.7021 6 14 0 0.00 0.00 - no Open
276 1.5261822919367496 -1.62124 -23.3378 6 10 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 -29.031kcal/mol
Ligand efficiency (LE) -1.9354kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -14.301
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 15HA

Physicochemical properties
Molecular weight 225.2Da
Lipinski: ≤ 500 Da
LogP (cLogP) -0.85
Lipinski: ≤ 5
Rotatable bonds 2

Conformational strain (MMFF94s)
Strain energy (ΔE) 17.63kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -84.72kcal/mol
Minimised FF energy -102.36kcal/mol

SASA & burial

✓ computed
SASA (unbound) 370.7Ų
Total solvent-accessible surface area of free ligand
BSA total 355.5Ų
Buried surface area upon binding
BSA apolar 171.0Ų
Hydrophobic contacts buried
BSA polar 184.5Ų
Polar contacts buried
Fraction buried 95.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 48.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1301.3Ų
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 2051.9Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 925.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)