FAIRMol

NMT-TY0824

Pose ID 14544 Compound 1750 Pose 306

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
T22
L. donovani rab5a L. donovani
Ligand NMT-TY0824

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 mixed SASA done
Strain ΔE
23.1 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.48, Jaccard 0.34, H-bond role recall 0.27
Burial
89%
Hydrophobic fit
67%
Reason: no major geometry red flags detected
5 protein-contact clashes 5 intramolecular clashes 60% of hydrophobic surface is solvent-exposed (6/10 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.535 kcal/mol/HA) ✓ Good fit quality (FQ -12.30) ✓ Strong H-bond network (14 bonds) ✓ Deep burial (89% SASA buried) ✓ Lipophilic contacts well-matched (67%) ✗ High strain energy (23.1 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (8)
Score
-27.623
kcal/mol
LE
-1.535
kcal/mol/HA
Fit Quality
-12.30
FQ (Leeson)
HAC
18
heavy atoms
MW
266
Da
LogP
0.15
cLogP
Strain ΔE
23.1 kcal/mol
SASA buried
89%
Lipo contact
67% BSA apolar/total
SASA unbound
445 Ų
Apolar buried
265 Ų

Interaction summary

HB 14 HY 1 PI 0 CLASH 5 ⚠ Exposure 60%

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
🚨Solvent-exposed hydrophobic surface — desolvation penalty likely
60% of hydrophobic surface is solvent-exposed (6/10 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Non-polar atoms 10 Buried (contacted) 4 Exposed 6 LogP 0.15 H-bonds 14
Exposed fragments: phenyl (6/6 atoms exposed)
Final rank3.435Score-27.623
Inter norm-1.682Intra norm0.148
Top1000noExcludedno
Contacts18H-bonds14
Artifact reasongeometry warning; 8 clashes; 2 protein clashes; moderate strain Δ 23.1
Residues
ALA24 ALA70 ASP68 GLN42 GLU43 GLU73 GLY23 GLY25 GLY47 GLY71 ILE46 LYS127 LYS26 SER22 SER27 SER28 THR44 THR69

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
NameRAB5AContacts21
PoseOpen native poseHB0
IFP residues
ALA158 ALA24 ALA40 ASN126 ASN41 ASP129 GLN42 GLU21 GLU73 GLY23 GLY25 LEU130 LEU39 LYS127 LYS159 LYS26 PHE38 SER157 SER22 SER27 SER28
Current overlap10Native recall0.48
Jaccard0.34RMSD-
HB strict4Strict recall0.27
HB same residue+role3HB role recall0.27
HB same residue3HB residue recall0.27

Protein summary

165 residues
Protein targetT22Atoms2561
Residues165Chains1
Residue summaryLEU:363; LYS:242; ALA:231; ARG:214; ILE:190; GLU:180; VAL:144; SER:143; PHE:140; ASN:112; THR:112; TYR:105; GLN:102; ASP:96; GLY:77; TRP:48

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
340 1.015571438451004 -1.5344 -25.1285 5 11 0 0.00 0.00 - no Open
306 3.435362664430664 -1.6822 -27.6233 14 18 10 0.48 0.27 - no Current
265 3.804863587511328 -1.36447 -23.1944 14 11 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 -27.623kcal/mol
Ligand efficiency (LE) -1.5346kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -12.299
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 18HA

Physicochemical properties
Molecular weight 266.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 0.15
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 23.07kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -47.69kcal/mol
Minimised FF energy -70.76kcal/mol

SASA & burial

✓ computed
SASA (unbound) 445.2Ų
Total solvent-accessible surface area of free ligand
BSA total 397.0Ų
Buried surface area upon binding
BSA apolar 265.2Ų
Hydrophobic contacts buried
BSA polar 131.8Ų
Polar contacts buried
Fraction buried 89.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 66.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1166.6Ų
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 1368.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 512.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)