FAIRMol

Z45956756

Pose ID 14773 Compound 3400 Pose 535

DB fairmolDocking 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 Z45956756

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
10.7 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.81, Jaccard 0.77, H-bond role recall 0.55
Burial
92%
Hydrophobic fit
86%
Reason: no major geometry red flags detected
2 protein-contact clashes 65% of hydrophobic surface is solvent-exposed (11/17 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
EcoTox / ADMET In-silico prediction only
Fish LC₅₀
Cat. 2 — Toxic (1–10 mg/L)
Daphnia EC₅₀
Cat. 2 — Toxic (1–10 mg/L)
Algae IC₅₀
Cat. 2 — Toxic (1–10 mg/L)
Bioaccum.
Not B (BCF≤2000)
Persistent
No
ADMET alerts (in-silico)
hERG Low Ames Clear DILI Low
Molecular report
Full metrics ↗
Weak Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.232 kcal/mol/HA) ✓ Good fit quality (FQ -10.31) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (92% SASA buried) ✓ Lipophilic contacts well-matched (86%) ✗ Moderate strain (10.7 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (10)
Score
-24.631
kcal/mol
LE
-1.232
kcal/mol/HA
Fit Quality
-10.31
FQ (Leeson)
HAC
20
heavy atoms
MW
263
Da
LogP
3.82
cLogP
Final rank
1.6652
rank score
Inter norm
-1.533
normalised
Contacts
18
H-bonds 10
Strain ΔE
10.7 kcal/mol
SASA buried
92%
Lipo contact
86% BSA apolar/total
SASA unbound
513 Ų
Apolar buried
402 Ų

Interaction summary

HBA 6 HY 2 PI 1 CLASH 2

HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 5.

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

HY · Hydrophobic contacts

CLASH · Clashes

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
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 overlap17Native recall0.81
Jaccard0.77RMSD-
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
535 1.6651671097078593 -1.53275 -24.6313 10 18 17 0.81 0.55 - no Current
544 2.0657735141787414 -1.22435 -19.5555 4 15 0 0.00 0.00 - no Open
524 2.188495864602808 -1.32388 -25.5093 7 14 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 -24.631kcal/mol
Ligand efficiency (LE) -1.2316kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -10.306
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 20HA

Physicochemical properties
Molecular weight 263.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 3.82
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 10.68kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 73.56kcal/mol
Minimised FF energy 62.88kcal/mol

SASA & burial

✓ computed
SASA (unbound) 513.1Ų
Total solvent-accessible surface area of free ligand
BSA total 469.7Ų
Buried surface area upon binding
BSA apolar 402.0Ų
Hydrophobic contacts buried
BSA polar 67.7Ų
Polar contacts buried
Fraction buried 91.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 85.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1305.8Ų
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 508.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)