FAIRMol

Z19138088

Pose ID 14608 Compound 651 Pose 370

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 Z19138088

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
28.7 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.67, Jaccard 0.64, H-bond role recall 0.64
Burial
73%
Hydrophobic fit
70%
Reason: no major geometry red flags detected
1 protein-contact clashes 64% of hydrophobic surface is solvent-exposed (16/25 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 (-0.810 kcal/mol/HA) ✓ Good fit quality (FQ -8.10) ✓ Strong H-bond network (10 bonds) ✓ Deep burial (73% SASA buried) ✓ Lipophilic contacts well-matched (70%) ✗ High strain energy (28.7 kcal/mol) ✗ Geometry warnings ✗ Many internal clashes (18)
Score
-27.538
kcal/mol
LE
-0.810
kcal/mol/HA
Fit Quality
-8.10
FQ (Leeson)
HAC
34
heavy atoms
MW
474
Da
LogP
4.20
cLogP
Strain ΔE
28.7 kcal/mol
SASA buried
73%
Lipo contact
70% BSA apolar/total
SASA unbound
731 Ų
Apolar buried
372 Ų

Interaction summary

HB 10 HY 4 PI 1 CLASH 1 ⚠ Exposure 64%

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
🚨Solvent-exposed hydrophobic surface — desolvation penalty likely
64% of hydrophobic surface is solvent-exposed (16/25 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 25 Buried (contacted) 9 Exposed 16 LogP 4.2 H-bonds 10
Exposed fragments: phenyl (6/6 atoms exposed)phenyl (4/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
Final rank3.781Score-27.538
Inter norm-0.979Intra norm0.170
Top1000noExcludedno
Contacts15H-bonds10
Artifact reasongeometry warning; 18 clashes; 2 protein clashes; moderate strain Δ 28.2
Residues
ALA158 ASN126 ASP129 GLU73 GLY23 GLY25 LEU130 LYS127 LYS128 LYS159 LYS26 PHE38 SER157 SER27 SER28

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 overlap14Native recall0.67
Jaccard0.64RMSD-
HB strict8Strict recall0.53
HB same residue+role7HB role recall0.64
HB same residue7HB residue recall0.64

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
435 1.9301717756467363 -0.72761 -23.752 6 16 0 0.00 0.00 - no Open
334 2.0263869649204853 -0.930222 -27.1777 3 21 0 0.00 0.00 - no Open
395 2.0501377984473983 -0.787007 -19.7508 5 14 0 0.00 0.00 - no Open
397 2.752858282721569 -0.800489 -23.9414 10 17 0 0.00 0.00 - no Open
396 2.7601535713818413 -0.591573 -16.9942 5 14 0 0.00 0.00 - no Open
381 2.9359635508409108 -0.793642 -19.3973 6 14 0 0.00 0.00 - no Open
450 3.1523302745872246 -0.760382 -22.134 3 18 0 0.00 0.00 - no Open
379 3.2188609293194674 -0.712407 -23.9203 8 17 0 0.00 0.00 - no Open
418 3.4321465037133247 -0.816749 -26.4904 4 18 0 0.00 0.00 - no Open
407 3.5524489581677203 -0.633858 -18.4382 7 15 0 0.00 0.00 - no Open
370 3.7807067079968997 -0.979467 -27.5375 10 15 14 0.67 0.64 - no Current
493 3.8486675627744926 -0.726729 -19.7364 7 15 0 0.00 0.00 - no Open
366 4.10912935177256 -0.834923 -27.5266 11 20 0 0.00 0.00 - no Open
336 4.160825631036783 -0.993151 -30.1156 5 15 0 0.00 0.00 - no Open
464 5.0362869852581325 -0.819442 -25.2435 6 21 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 -27.538kcal/mol
Ligand efficiency (LE) -0.8099kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -8.104
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 34HA

Physicochemical properties
Molecular weight 474.5Da
Lipinski: ≤ 500 Da
LogP (cLogP) 4.20
Lipinski: ≤ 5
Rotatable bonds 7

Conformational strain (MMFF94s)
Strain energy (ΔE) 28.66kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 86.00kcal/mol
Minimised FF energy 57.34kcal/mol

SASA & burial

✓ computed
SASA (unbound) 731.0Ų
Total solvent-accessible surface area of free ligand
BSA total 533.4Ų
Buried surface area upon binding
BSA apolar 372.2Ų
Hydrophobic contacts buried
BSA polar 161.2Ų
Polar contacts buried
Fraction buried 73.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 69.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -1360.1Ų
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 547.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)