FAIRMol

NMT-TY0622

Pose ID 7720 Compound 524 Pose 268

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
T12
T. brucei R5P T. brucei
Ligand NMT-TY0622
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 high Native strong SASA done
Strain ΔE
22.9 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.88, Jaccard 0.88, H-bond role recall 0.40
Burial
73%
Hydrophobic fit
71%
Reason: no major geometry red flags detected
2 protein-contact clashes 40% of hydrophobic surface appears solvent-exposed (6/15 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.127 kcal/mol/HA) ✓ Good fit quality (FQ -10.25) ✓ Strong H-bond network (10 bonds) ✓ Deep burial (73% SASA buried) ✓ Lipophilic contacts well-matched (71%) ✗ High strain energy (22.9 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (7)
Score
-28.179
kcal/mol
LE
-1.127
kcal/mol/HA
Fit Quality
-10.25
FQ (Leeson)
HAC
25
heavy atoms
MW
381
Da
LogP
1.77
cLogP
Strain ΔE
22.9 kcal/mol
SASA buried
73%
Lipo contact
71% BSA apolar/total
SASA unbound
600 Ų
Apolar buried
310 Ų

Interaction summary

HB 10 HY 6 PI 2 CLASH 2 ⚠ Exposure 40%

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
⚠️Partial hydrophobic solvent exposure
40% of hydrophobic surface appears solvent-exposed (6/15 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 15 Buried (contacted) 9 Exposed 6 LogP 1.77 H-bonds 10
Exposed fragments: phenyl (6/6 atoms exposed)
Final rank3.643Score-28.179
Inter norm-1.152Intra norm0.025
Top1000noExcludedno
Contacts14H-bonds10
Artifact reasongeometry warning; 7 clashes; 3 protein clashes; moderate strain Δ 22.9
Residues
ARG140 ARG144 ASN106 HIS105 HIS141 ARG46 ASP13 CYS72 GLY73 GLY77 HIS14 ILE15 SER74 TYR49

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name6FXSContacts16
PoseOpen native poseHB0
IFP residues
ARG140 ARG144 ASN106 HIS105 HIS141 ARG46 ASP13 CYS72 GLY73 GLY75 GLY77 HIS14 ILE15 ILE76 SER74 TYR49
Current overlap14Native recall0.88
Jaccard0.88RMSD-
HB strict6Strict recall0.50
HB same residue+role4HB role recall0.40
HB same residue5HB residue recall0.50

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
308 0.3842150656616825 -0.951549 -25.0395 4 17 0 0.00 0.00 - no Open
276 1.2600618081157402 -1.12204 -28.7499 9 15 0 0.00 0.00 - no Open
288 1.7018393222780244 -1.13668 -28.6792 9 14 0 0.00 0.00 - no Open
352 1.9271195694416656 -1.10716 -29.8519 6 13 0 0.00 0.00 - no Open
341 1.927730112535267 -0.859185 -22.1976 9 12 0 0.00 0.00 - no Open
273 1.9961552376915304 -1.35584 -31.5197 14 17 0 0.00 0.00 - no Open
327 2.0961391154894002 -0.86609 -19.9983 5 13 0 0.00 0.00 - no Open
392 2.3248094781583672 -0.940735 -21.0428 11 16 0 0.00 0.00 - no Open
308 2.8353655663354234 -1.13363 -28.9578 5 19 0 0.00 0.00 - no Open
378 2.966730885309019 -1.23963 -28.1056 8 15 0 0.00 0.00 - no Open
423 3.5162080347453757 -1.16596 -29.4186 9 16 0 0.00 0.00 - no Open
361 3.58426702200673 -1.22019 -28.4754 6 15 0 0.00 0.00 - no Open
268 3.6431928517433407 -1.15199 -28.179 10 14 14 0.88 0.40 - no Current
327 3.7246234846293826 -1.02174 -24.8257 12 17 0 0.00 0.00 - no Open
347 3.9186485478235458 -1.05383 -26.5042 6 19 0 0.00 0.00 - no Open
269 4.208957465627367 -1.25064 -26.887 9 18 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 -28.179kcal/mol
Ligand efficiency (LE) -1.1272kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.247
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 25HA

Physicochemical properties
Molecular weight 381.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.77
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 22.91kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -94.12kcal/mol
Minimised FF energy -117.03kcal/mol

SASA & burial

✓ computed
SASA (unbound) 600.4Ų
Total solvent-accessible surface area of free ligand
BSA total 438.0Ų
Buried surface area upon binding
BSA apolar 310.2Ų
Hydrophobic contacts buried
BSA polar 127.8Ų
Polar contacts buried
Fraction buried 72.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 70.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -2129.0Ų
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 762.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)