Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
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Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak
SASA cached
Weak or marginal quality
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
15.8 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.76, Jaccard 0.64, H-bond role recall 0.09
Reason: no major geometry red flags detected
4 protein-contact clashes
4 intramolecular clashes
48% of hydrophobic surface appears solvent-exposed (11/23 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.872 kcal/mol/HA)
✓ Good fit quality (FQ -8.57)
✓ Good H-bonds (5 bonds)
✓ Deep burial (71% SASA buried)
✓ Lipophilic contacts well-matched (73%)
✗ Moderate strain (15.8 kcal/mol)
✗ Geometry warnings
✗ Protein-contact clashes (9)
✗ Many internal clashes (16)
Score
-27.895
kcal/mol
LE
-0.872
kcal/mol/HA
Fit Quality
-8.57
FQ (Leeson)
HAC
32
heavy atoms
MW
466
Da
LogP
4.94
cLogP
Interaction summary
HB 5
HY 8
PI 0
CLASH 4
⚠ Exposure 47%
Interaction summary
HB 5
HY 8
PI 0
CLASH 4
⚠ Exposure 47%
Partial hydrophobic solvent exposure
48% of hydrophobic surface appears solvent-exposed (11/23 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 23
Buried (contacted) 12
Exposed 11
LogP 4.94
H-bonds 5
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (5 atoms exposed)
| Final rank | 2.276 | Score | -27.895 |
|---|---|---|---|
| Inter norm | -0.951 | Intra norm | 0.080 |
| Top1000 | no | Excluded | no |
| Contacts | 20 | H-bonds | 5 |
| Artifact reason | geometry warning; 16 clashes; 9 protein contact clashes | ||
| Residues |
ALA24
ALA40
ASN41
GLN42
GLU43
GLU73
GLY23
GLY25
GLY71
LEU130
LEU39
LYS127
LYS159
LYS26
PHE38
SER22
SER27
SER28
THR44
THR69
| ||
Protein summary
165 residues
| Protein target | T22 | Atoms | 2561 |
|---|---|---|---|
| Residues | 165 | Chains | 1 |
| Residue summary | LEU: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 | ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | RAB5A | Contacts | 21 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA158
ALA24
ALA40
ASN126
ASN41
ASP129
GLN42
GLU21
GLU73
GLY23
GLY25
LEU130
LEU39
LYS127
LYS159
LYS26
PHE38
SER157
SER22
SER27
SER28
| ||
| Current overlap | 16 | Native recall | 0.76 |
| Jaccard | 0.64 | RMSD | - |
| HB strict | 2 | Strict recall | 0.13 |
| HB same residue+role | 1 | HB role recall | 0.09 |
| HB same residue | 1 | HB residue recall | 0.09 |
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 40 | 0.6318633434685462 | -1.05679 | -25.2363 | 11 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 32 | 1.1093340137788317 | -0.854228 | -26.2704 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 33 | 1.221046822080138 | -0.8404 | -24.6948 | 5 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 12 | 2.2763008769763395 | -0.951446 | -27.8948 | 5 | 20 | 16 | 0.76 | 0.09 | - | no | Current |
| 41 | 2.7017944339236353 | -0.816536 | -24.4886 | 6 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 19 | 2.8062455719099972 | -0.858902 | -22.2054 | 6 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 17 | 2.9889278715837735 | -1.00267 | -19.7644 | 8 | 23 | 0 | 0.00 | 0.00 | - | no | Open |
| 35 | 3.4599440764772713 | -0.8945 | -24.7699 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 30 | 3.771422856064557 | -0.787662 | -23.0094 | 6 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 31 | 4.092882811740988 | -0.838847 | -22.2153 | 6 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 35 | 4.104329269165856 | -0.708066 | -24.0235 | 9 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 29 | 4.699770164678327 | -1.04112 | -26.4163 | 8 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 22 | 4.76668917309497 | -0.781504 | -15.2577 | 9 | 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.
Scoring & efficiency
Docking score
-27.895kcal/mol
Ligand efficiency (LE)
-0.8717kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.572
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
32HA
Physicochemical properties
Molecular weight
466.0Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.94
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
15.80kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
10.80kcal/mol
Minimised FF energy
-5.00kcal/mol
SASA & burial
✓ computed
SASA (unbound)
782.6Ų
Total solvent-accessible surface area of free ligand
BSA total
557.9Ų
Buried surface area upon binding
BSA apolar
406.3Ų
Hydrophobic contacts buried
BSA polar
151.6Ų
Polar contacts buried
Fraction buried
71.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
72.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1394.8Ų
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
595.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)