FAIRMol

NMT-TY0959

Pose ID 14564 Compound 527 Pose 326

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-TY0959

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
39.6 kcal/mol
Protein clashes
0
Internal clashes
11
Native overlap
contact recall 0.76, Jaccard 0.62, H-bond role recall 0.18
Burial
88%
Hydrophobic fit
71%
Reason: 11 internal clashes
11 intramolecular clashes 59% of hydrophobic surface appears solvent-exposed (10/17 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 (-1.153 kcal/mol/HA) ✓ Good fit quality (FQ -10.75) ✓ Strong H-bond network (10 bonds) ✓ Deep burial (88% SASA buried) ✓ Lipophilic contacts well-matched (71%) ✗ Very high strain energy (39.6 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (11)
Score
-31.119
kcal/mol
LE
-1.153
kcal/mol/HA
Fit Quality
-10.75
FQ (Leeson)
HAC
27
heavy atoms
MW
403
Da
LogP
2.03
cLogP
Strain ΔE
39.6 kcal/mol
SASA buried
88%
Lipo contact
71% BSA apolar/total
SASA unbound
633 Ų
Apolar buried
391 Ų

Interaction summary

HB 10 HY 6 PI 1 CLASH 0 ⚠ Exposure 58%

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
No clash · clashes detected for this pose.
⚠️Partial hydrophobic solvent exposure
59% of hydrophobic surface appears solvent-exposed (10/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 17 Buried (contacted) 7 Exposed 10 LogP 2.03 H-bonds 10
Exposed fragments: phenyl (6/6 atoms exposed)phenyl (4/6 atoms exposed)
Final rank1.977Score-31.119
Inter norm-1.134Intra norm-0.019
Top1000noExcludedno
Contacts21H-bonds10
Artifact reasongeometry warning; 11 clashes; 1 protein clash; high strain Δ 39.3
Residues
ALA158 ALA24 ALA70 ASN126 ASP129 GLN42 GLU43 GLU73 GLY23 GLY25 GLY71 LEU130 LYS127 LYS159 LYS26 PHE38 SER157 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 overlap16Native recall0.76
Jaccard0.62RMSD-
HB strict2Strict recall0.13
HB same residue+role2HB role recall0.18
HB same residue4HB residue recall0.36

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
350 0.3629211958252925 -0.926251 -24.8853 2 13 0 0.00 0.00 - no Open
308 0.8712687604222177 -1.14475 -30.9484 7 15 0 0.00 0.00 - no Open
313 1.3142726160638258 -1.30957 -33.6603 12 15 0 0.00 0.00 - no Open
337 1.7652358533706136 -0.983958 -24.6706 6 21 0 0.00 0.00 - no Open
326 1.9773175739360493 -1.1336 -31.1195 10 21 16 0.76 0.18 - no Current
291 2.165473959343045 -1.26034 -34.3636 9 22 0 0.00 0.00 - no Open
301 2.480529293523874 -1.03512 -28.7525 9 12 0 0.00 0.00 - no Open
391 2.9008417563283935 -1.06217 -28.0759 7 15 0 0.00 0.00 - no Open
405 2.9806369013586718 -1.18262 -29.8648 6 15 0 0.00 0.00 - no Open
381 3.0321874169205607 -1.08611 -28.6887 6 16 0 0.00 0.00 - no Open
379 3.2808649478445537 -0.969429 -25.6956 10 17 0 0.00 0.00 - no Open
332 3.3588118370115048 -1.08116 -27.9486 7 17 1 0.05 0.00 - no Open
416 3.387046221950613 -0.924839 -25.7132 8 13 0 0.00 0.00 - no Open
334 3.429500560915679 -1.04914 -24.4852 8 15 0 0.00 0.00 - no Open
349 3.654496302035269 -0.850128 -21.98 8 14 0 0.00 0.00 - no Open
302 3.8731875216797746 -1.1408 -30.4082 8 22 0 0.00 0.00 - no Open
286 4.0813402406540185 -0.908062 -25.3939 13 15 0 0.00 0.00 - no Open
358 4.09740218547716 -0.710564 -18.8071 6 10 0 0.00 0.00 - no Open
336 4.132326379777683 -0.942975 -24.3804 7 17 0 0.00 0.00 - no Open
453 4.769829786717276 -1.02855 -27.026 8 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 -31.119kcal/mol
Ligand efficiency (LE) -1.1526kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.753
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 27HA

Physicochemical properties
Molecular weight 403.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.03
Lipinski: ≤ 5
Rotatable bonds 8

Conformational strain (MMFF94s)
Strain energy (ΔE) 39.64kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy -11.10kcal/mol
Minimised FF energy -50.74kcal/mol

SASA & burial

✓ computed
SASA (unbound) 632.9Ų
Total solvent-accessible surface area of free ligand
BSA total 553.6Ų
Buried surface area upon binding
BSA apolar 390.6Ų
Hydrophobic contacts buried
BSA polar 163.0Ų
Polar contacts buried
Fraction buried 87.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 70.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1307.3Ų
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 1368.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 506.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)