FAIRMol

Z49604831

Pose ID 14606 Compound 1222 Pose 368

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 Z49604831

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject SASA cached
Promising but geometrically suspicious
Binding strong Geometry low Native strong SASA done
Strain ΔE
51.1 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.86, Jaccard 0.75, H-bond role recall 0.55
Burial
90%
Hydrophobic fit
73%
Reason: strain 51.1 kcal/mol
strain ΔE 51.1 kcal/mol 3 protein-contact clashes 3 intramolecular clashes 58% of hydrophobic surface appears solvent-exposed (11/19 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Full metrics ↗
Reject Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-1.224 kcal/mol/HA) ✓ Good fit quality (FQ -11.56) ✓ Strong H-bond network (12 bonds) ✓ Deep burial (90% SASA buried) ✓ Lipophilic contacts well-matched (73%) ✗ Extreme strain energy (51.1 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (7)
Score
-34.274
kcal/mol
LE
-1.224
kcal/mol/HA
Fit Quality
-11.56
FQ (Leeson)
HAC
28
heavy atoms
MW
403
Da
LogP
2.52
cLogP
Strain ΔE
51.1 kcal/mol
SASA buried
90%
Lipo contact
73% BSA apolar/total
SASA unbound
659 Ų
Apolar buried
432 Ų

Interaction summary

HB 12 HY 9 PI 1 CLASH 3 ⚠ Exposure 57%

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
58% of hydrophobic surface appears solvent-exposed (11/19 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 19 Buried (contacted) 8 Exposed 11 LogP 2.52 H-bonds 12
Exposed fragments: phenyl (6/6 atoms exposed)phenyl (4/5 atoms exposed)aliphatic chain/group (1 atom exposed)
Final rank4.432Score-34.274
Inter norm-1.245Intra norm0.021
Top1000noExcludedno
Contacts21H-bonds12
Artifact reasongeometry warning; 7 clashes; 3 protein clashes; high strain Δ 51.0
Residues
ALA158 ALA24 ALA40 ASN126 ASN41 ASP129 GLN42 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 overlap18Native recall0.86
Jaccard0.75RMSD-
HB strict7Strict recall0.47
HB same residue+role6HB role recall0.55
HB same residue6HB residue recall0.55

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
383 0.20298815758912536 -1.17436 -32.5023 7 15 0 0.00 0.00 - no Open
412 1.9755085550443252 -0.955179 -32.4049 4 14 0 0.00 0.00 - no Open
368 4.432401315740646 -1.2451 -34.2741 12 21 18 0.86 0.55 - 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 -34.274kcal/mol
Ligand efficiency (LE) -1.2241kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -11.556
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 28HA

Physicochemical properties
Molecular weight 403.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 2.52
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 51.09kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 51.61kcal/mol
Minimised FF energy 0.52kcal/mol

SASA & burial

✓ computed
SASA (unbound) 658.5Ų
Total solvent-accessible surface area of free ligand
BSA total 589.4Ų
Buried surface area upon binding
BSA apolar 431.5Ų
Hydrophobic contacts buried
BSA polar 157.8Ų
Polar contacts buried
Fraction buried 89.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 73.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1356.9Ų
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 1368.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 500.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)