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 high
Native strong
SASA done
Strain ΔE
25.1 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.71, Jaccard 0.62, H-bond role recall 0.36
Reason: no major geometry red flags detected
1 protein-contact clashes
40% of hydrophobic surface appears solvent-exposed (6/15 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 (-1.367 kcal/mol/HA)
✓ Good fit quality (FQ -11.87)
✓ Strong H-bond network (11 bonds)
✓ Deep burial (92% SASA buried)
✓ Lipophilic contacts well-matched (63%)
✗ High strain energy (25.1 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (10)
Score
-30.079
kcal/mol
LE
-1.367
kcal/mol/HA
Fit Quality
-11.87
FQ (Leeson)
HAC
22
heavy atoms
MW
302
Da
LogP
1.99
cLogP
Interaction summary
HB 11
HY 2
PI 1
CLASH 1
⚠ Exposure 40%
Interaction summary
HB 11
HY 2
PI 1
CLASH 1
⚠ Exposure 40%
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
40% of hydrophobic surface appears solvent-exposed (6/15 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 15
Buried (contacted) 9
Exposed 6
LogP 1.99
H-bonds 11
Exposed fragments:
phenyl (6/6 atoms exposed)
| Final rank | 5.152 | Score | -30.079 |
|---|---|---|---|
| Inter norm | -1.445 | Intra norm | 0.078 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 11 |
| Artifact reason | geometry warning; 10 clashes; 5 protein clashes; moderate strain Δ 25.1 | ||
| Residues |
ALA24
ALA40
ASN126
ASN41
GLN42
GLU73
GLY23
GLY25
GLY71
LEU39
LYS127
LYS26
PHE38
SER22
SER27
SER28
THR44
THR69
| ||
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 | 15 | Native recall | 0.71 |
| Jaccard | 0.62 | RMSD | - |
| HB strict | 4 | Strict recall | 0.27 |
| HB same residue+role | 4 | HB role recall | 0.36 |
| HB same residue | 4 | HB residue recall | 0.36 |
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 | ||
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 559 | 0.7198418180090042 | -0.933488 | -20.4818 | 6 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 525 | 2.4172194168614993 | -1.48041 | -32.0363 | 9 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 512 | 2.545937422647049 | -1.61802 | -34.0323 | 11 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 567 | 2.9952729829901434 | -1.24945 | -25.8165 | 9 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 524 | 3.422947619134114 | -1.36673 | -26.6001 | 13 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 550 | 3.750956682432338 | -1.21808 | -25.8403 | 6 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 582 | 4.472569139535506 | -1.15982 | -25.4195 | 9 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 529 | 4.491059808940537 | -1.52163 | -29.8977 | 11 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 541 | 5.152210004952779 | -1.44518 | -30.0794 | 11 | 18 | 15 | 0.71 | 0.36 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-30.079kcal/mol
Ligand efficiency (LE)
-1.3672kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.870
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
22HA
Physicochemical properties
Molecular weight
302.2Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.99
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
25.15kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
95.98kcal/mol
Minimised FF energy
70.83kcal/mol
SASA & burial
✓ computed
SASA (unbound)
483.4Ų
Total solvent-accessible surface area of free ligand
BSA total
445.6Ų
Buried surface area upon binding
BSA apolar
279.4Ų
Hydrophobic contacts buried
BSA polar
166.2Ų
Polar contacts buried
Fraction buried
92.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
62.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1169.3Ų
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
512.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)